Tax Operations Playbook
Streamline your tax operations with essential processes and guidelines for effective management.
The intent of this Playbook is to provide an outline for the basics of the Tax Operations and the Activation Tax Operations teams’ processes. We will continue to develop and iterate on these processes over time as our product is grown and enhanced. We hope to answer your questions here but are always available through our help center should you have any additional questions or need for assistance.
Applied For Tax IDs - Payment Processing
In the majority of states a Tax ID is required for a payment submission. When the Tax ID for a tax is set to ‘Applied For’ it cannot be included in an ACH file and also may not be allowed as a paper check submission. Check will take the following actions when a tax liability has reached its due date but the Tax ID is marked as ‘Applied For’:
- When the due date has been reached, Check will make every attempt to submit the payment via a paper check. We cannot guarantee the agency will accept the payment once it has been received.
- In the event there are tax payments that cannot be submitted to the appropriate agency due to the missing information, Check will process a refund back to the company by the 15th of the second month following the filing quarter (March 15th, June 15th, September 15th, December 15th).
If the company received a refund from Check of their tax liability and they now have the respective Tax ID, they will have two options:
- Check can recollect the amount that was refunded and send the funds to the agency on their behalf. It’s important to note, there may be a second collection required as we won’t know the amount of agency assigned penalty and interest unless a tax notice is received before the time of collection.
- The company can remit the payment directly to the agency on their own behalf.
The best practice is for companies to register for any and all applicable taxes as soon as they are aware they will hire an employee in a new state or locality. Some states may have certain limitations as to when you can actually register so be sure to check out their website for the actual requirements. You may also review our guides on new company registration.
Applied For Tax IDs - Tax Return Processing
A Tax ID is required for an electronic filing submission. When the Tax ID for a tax is set to ‘Applied For’ it cannot be included in an e-File. In addition, agencies are rapidly moving away from accepting any type of paper return and have become very strict in regards to a paper return with an ‘Applied For’ account number. Check will make every attempt to mail a paper return but cannot guarantee the agency will accept the return once it has been received. If the agency will not accept a paper return the company will be added to the Partner’s Filing Failure spreadsheet.
We highly recommend companies register for any and all applicable taxes as soon as they are aware they will hire an employee in a new state or locality. Please refer to our Knowledge Base for agency by agency instructions for the registration process.
Quarter-End Deadlines
The following quarter-end deadlines will apply to all companies:
Missing Tax IDs, TPA assignments, and correcting entries must be completed no later than the fourth business day following the end of the quarter. We cannot guarantee a timely filing submission or payment in the event this information is not received by the noted deadline. Also of note, there are a small number of agencies that will not allow any type of filing, including a paper submission, without a proper Tax ID.
In the event there are tax payments that cannot be submitted to the appropriate agency due to the missing information, Check will process a refund back to the company by the 15th of the second month following the filing quarter (March 15th, June 15th, September 15th, December 15th).
The following timeline will be followed when the filing month has been reached (January, April, July, October). Please note that dates may fluctuate if the deadline falls on a non-business day -
- The 1st of the month - import & post the quarterly file
- The first week of the month - balance and post corrections for any out-of-balance entries (aka variances)
- 7th of the month- - delivery of variances to Partners
- 9th of the month- deliver company packages to include a Reconciliation Recap that will assist in explaining the out-of-balance corrections completed.
- 10th of the month - variance refund and/or collection is processed
- Once balancing is complete - file returns, prioritized by due date, payment method (example, debit payments that include a variance will wait until after variances are collected), and single file upload states. Print checks and tax returns that are submitted via paper. This will include any returns for which the Tax ID is ‘Applied For’ AND the agency accepts a paper return submission.
The following exceptions to the above noted timeline will include -
- Companies with a funding failure (see Funding Failure for further information)
- Company escalations - We understand there are times when a company may need to be an exception to the standard timeline due to an escalated state. These escalations will be discussed by the Partner’s management team and the Tax Operations manager and to determine the best path forward.
Third-Party Administrator Rights
Third-Party Administrator rights are commonly referred to as TPA. In this definition of TPA, we are referring to a process that must be completed by the company with the purpose of allowing Check to file a company’s tax returns and remit payment for the returns filed. There are a handful of states that will not allow a Payroll Provider to file tax returns without the company completing an action using their own account login. These state taxes are CO PFML, HI SUI, MN SUI, and NM SUI. This isn’t to say other states won’t have their own unique data requirements, but in the case of these states, Check cannot file a tax return without the company completing the required steps. During the Activation process, Check will identify if the company is in one of the states noted above. The Activation communication will include a notification that TPA is required. In addition, as part of the TaxOps team’s quarterly preparation, the following steps will be completed:
- In the month prior to quarter end, a review of each agency site will be conducted to identify companies that have not completed the TPA assignment and a Zendesk ticket will be sent to the Partner identifying the company and the missing jurisdiction.
- If the TPA assignment is still not completed at the time of filing, the return will be rejected by the agency and the company will be added to the Partner’s Filing Failure spreadsheet.
Filing Failure
The TaxOps team at Check will begin filing tax returns in the month following quarter-end. The majority of our tax returns are filed electronically via a bulk file upload. During the filing process, agencies will provide a response, typically within 24 hours, to confirm that the file was uploaded. This is when Check is able to identify Filing Failures and the process of building out a Partner specific spreadsheet begins. This spreadsheet is shared immediately and updated on a daily basis as agency responses are received.
Filing Failures can occur for a variety of reasons. The term is used to describe an electronic tax return filing that was rejected by the agency during the submission process. Common reasons for filing failures are:
- Applied For/Invalid Tax ID - The company either has not registered for an account number or has not provided one to Check.
- Already filed - The company didn’t properly offboard from their previous Payroll Provider and that Payroll Provider completed the filing, or the company has ceased processing payroll and did not submit a notice of the termination.
- TPA Failure - (See Third-Party Administrator Rights) This was either not completed or a step was missed during the attempt to complete it.
- Inactive account - Either an invalid Tax ID was provided by the company or the agency has closed the account due to inactivity.
- One or more prior quarters is missing - The agency will not allow a filing when a prior quarter hasn’t been filed. This is specific to Louisiana Unemployment.
- Invalid Tax Rate - The agency will not allow a return submission with an incorrect tax rate. This is specific to Oklahoma Unemployment.
- Partial Failure/Invalid SSN - The agency will not accept a tax return with an invalid Social Security number. The wage data was updated to remove the employee wages that were to be reported under the invalid Social Security number. This means the employee was not reported to the applicable agency along with the associated wage detail.
- Missing Historical Data - A state may require the tax return filing to reflect each tax payment that was paid to them in the quarter. When the return is filed and it does not reconcile, the agency will reject the return.
Check will attempt to send a paper return when a filing failure is encountered. Tax agencies are rapidly moving away from accepting a paper tax return which makes this a haphazard solution at best. The ideal solution is for the company to correct the filing blocker so the return can be submitted electronically. The resolution for the common situations noted above are:
- Applied For Tax ID - Provide the account number immediately upon receipt. The Partner should then notify Check via a Support ticket that the information has been provided and to request a reattempt of the filing.
- Already filed - Upon enrollment and Activation, the company should immediately notify the previous Payroll Provider to cease all functions on their behalf. They should then obtain a copy of the return that was filed as an amended filing now has to be completed that will include both the information filed by the previous Payroll Provider and the information that was processed through Check. If this is an existing company that ceased processing payroll, they should submit a termination notification.
- POA/TPA Failure -
- The company should immediately complete the TPA assignment.
- If this is a POA failure, a new POA is required and it must be signed by the Owner/Officer of the company. POA failures are a direct result of an invalid signature.
- Once resolved, the Partner should then notify Check via a Support ticket that the TPA assignment has been completed or a newly signed POA has been received and to request a reattempt of the filing.
- Inactive account - The company must validate the account number. If the account number is accurate it is necessary for the company to contact the state and reactivate their account. The Partner should then notify Check via a Support ticket that the issue has been resolved and to request a reattempt of the filing.
- One or more prior quarters is missing - Either the date of registration should be corrected to remove the requirement for the prior quarter filing or a filing must be completed. Check will not file returns on periods before the company’s first processing quarter. When the issue is resolved, the Partner should then notify Check via a Support ticket that the issue has been resolved and to request a reattempt of the filing.
- Invalid Tax Rate - The company should immediately supply the valid tax rate for the current year.
- Partial Failure/Invalid SSN - The company should immediately obtain a valid SSN from the employee.
- Missing Historical Data - Deposit reports and/or payroll reports should be re-requested from the company to identify what was missed in the original implementation.
Current filings will take priority over a filing failure. After all current filings are completed, the TaxOps team will circle back on all resolved failures and make every reasonable attempt to refile a return before its due date. Should the due date not be met, Check will not be responsible for any penalty and/or interest associated with the original failure.
Failed Funding
When a company has a funding failure that remains unfunded, Check will process a termination of services for that company. A failure to fund payroll will be considered a breach of contract, thus nullifying Check’s obligation to pay and file tax returns on the company’s behalf. If the payroll remains unfunded after 30 days, Check reserves the right to take further action including but not limited to terminating all payroll services for the employer.
The company will be placed into a held status and no tax returns will be issued. Should the company fund the payroll, we will resume processing for them, including filing untimely returns and remitting tax liabilities. Any late filing penalties will be the company's responsibility to pay.
If funding is not received, the process below will be followed:
- All funded employee withholding (income tax) taxes will be remitted to the appropriate taxing authorities. In the event the employer has not provided a Tax ID, the funds will be returned to the employer.
- All other funded employer taxes will be refunded directly to the employer.
- Check will not process any current quarter or annual tax returns on an employer’s behalf. The company will be terminated in Check and removed from our Partners' view in Console.
- A revocation of Form 8655 will be processed by Check to the IRS and state company listings will be processed to show the company is no longer with Check.
- The following communication will be sent to our Partner -
Hello,
COMPANY NAME has failed to fund their XX/XX/202X payroll and has been unresponsive to our collection attempts, resulting in a termination of service with Check. All pending funded tax liabilities will be refunded immediately, and the company will be responsible to remit and file QX 202X taxes directly to the appropriate agencies.
Please note that QX 202X returns will not be filed.
A refund of $XXX.XX will be processed back to the company immediately.
‘1099 Only’ to W2 Employer Handling
The differences between a ‘1099 Only’ company and a W2 employer are small but important in regards to payroll tax processing. While it is not necessary for a ‘1099 Only’ company to have a second business verification review, it is necessary for that company to be reviewed at a payroll tax level. The Activation team will look at such things as Tax IDs, tax payment frequencies, unemployment tax rates, TPA requirements, etc. As such, when at least one W2 employee is added to a company which was initially implemented as a ‘1099 Only’ entity, the Activation team will receive an internal notification and an expedited review will begin. Check understands how critical the ability to run payroll is and will process these companies as quickly as possible. After the review is completed, the Partner will receive an Activation communication outlining any necessary actions to be completed.
Mid-Quarter Collections
It is common for a company to switch Payroll Providers midway through the year. This can happen at any point during the year and isn’t restricted to the beginning of a quarter. When a company decides to leave their previous Payroll Provider, there are frequently payroll taxes that were accrued but remain unpaid because the due dates haven’t been reached at the time of the company’s departure. Check on the other hand, will be processing payroll for the company when the due date is reached. This means Check needs to process a collection of any unpaid tax liabilities in order to have the funding to remit those payments on a company’s behalf. This collection is known as a “Mid-Quarter Collection”.
Mid-Quarter Collection usually includes state unemployment, federal unemployment, and local taxes but it can also include federal and state income taxes based on the company’s first check date and the due dates of the tax liability. During the Activation process, our team will identify and communicate to the Partner the amount of the expected collection. This amount is open for discussion based on whether the previous provider made the deposits and should be reviewed by both the Partner and the company! If the company indicates a tax was in fact paid by their previous provider, the collection amount will be adjusted to remove that item from the total.
The collection is scheduled for the first business day of the month following the company’s start date. For example, a company that starts on February 15th will have a Mid-Quarter Collection processed on March 1st (assuming the first is not a weekend). Because the Mid-Quarter Collection can include income taxes that are paid on a monthly payment frequency, it is important to note that a company starting later in the month would still have the same due date. This ensures Check is properly funded for all pending tax payments and avoids late payment penalties.
No Start
A No Start occurs when a company has been fully implemented and submitted to the Activation team, their first check date is scheduled, but they have not run their first payroll on the scheduled first check date. They may intend to process payroll through Check and are simply pushing their first check date out, but when this occurs Check must evaluate if their new first check date crosses a month, quarter, or a year. If and when it is determined that the first check date does in fact cross from one quarter or year into another, there are steps that will have to be completed by the company. It should also be understood that Check will not file any tax returns for the quarter or year for their original first check date. Check’s filing obligations will begin when the company begins processing payroll on our API.
The steps to be completed are the following:
- Check will delete any completed Powers of Attorney. The company will need to sign new forms that reflect the updated month, quarter or year for which they begin processing.
- If additional payroll history is required, it must be loaded by the Partner and then reviewed by the Activation team.
- Any previously scheduled Mid-Quarter Collections will be canceled and a new review completed to determine if a collection is required and the updated amount to be collected will be communicated to the Partner.
Company Terminations
Ideally, a company is 100% satisfied with their payroll offering and never chooses to move to another Payroll Provider. When a company chooses to move to another Payroll Provider or if they cease operating entirely, there is specific information needed in regards to payroll tax filings that will have to be gathered from the company.
- What is the final payroll check date processed with our Partner through the Check API?
- Will Check be expected to file the current quarter’s quarterly/annual tax returns on the company’s behalf?
- If the answer is no, a refund will be issued for the unpaid accrued taxes.
- If the answer is yes, Check will process all of the current quarter returns. Depending on the time of year, there may still be a refund issued to the company for taxes that are due at a later date. For example, if the company ceases processing with our Partner at the end of Q2 but federal unemployment (FUTA) has an annual tax payment frequency, a refund of all accrued FUTA taxes will be completed.
- Is the company moving to another Payroll Provider?
- The company/Partner will be provided a list of expected tax returns and they must return a defined list of the returns that will and will not be marked as final (company-reporting states for state unemployment would not be marked as final).
- If yes, is the new Payroll Provider a Professional Employer Organization (PEO)?
- If yes, will Check be filing the annual returns and W2s at the end of the year?
- If yes, will Check be marking those returns as final?
- Is the company ceasing business?
- If yes, will Check be filing the annual returns at the end of the year?
- If yes, will Check be marking those returns as final?
The answers to these questions will ensure all tax returns and tax payments are properly processed and any applicable refunds are handled appropriately.
Invalid SSNs
There are basic SSN errors that are outlined by the Social Security Administration (SSA) and enforced by Check’s tax filing software. These validations include the following:
- The first segment of 3 digits is 000, 666, or in the 900 series,
- The second segment of 2 digits is 00, and/or
- The third segment of 4 digits is 0000
In addition, the following SSNs are considered to be dummy numbers:
000000000, 1111111111, 222222222, 333333333, 444444444, 555555555, 666666666, 777777777, 888888888, 999999999, 123456789, 987654321
It is incumbent on the Partner to contact the company and notify them of the invalid SSN. The SSN must be corrected prior to the Quarter-End Deadline.
If the SSN is not corrected there are several areas that can and will be affected.
- Quarterly Wage Reporting - Unemployment returns require a valid SSN. There are several states that will not allow any type of invalid or dummy SSN reporting. These invalid wage records will be removed from the original filing and an amended return will be required when the valid SSN is provided. In the event the state does allow invalid or dummy SSN reporting, an amended return will still be required to correct the SSN.
- This in turn will affect the employee’s ability to file for unemployment should that employee be terminated or laid off. As no wages were reported for them, they cannot claim unemployment until the issue has been resolved.
- Annual Wage Reporting - The SSA will allow for a W2 to be created with all zeroes only (0000-00-0000). When an invalid or dummy SSN is identified at year-end, it will be replaced with all zeroes. This will allow Check to file the W2 and W3 annual returns with the SSA. This does not remove the requirement to file with a valid SSN and the W2 will have to be corrected by issuing a W2C.
Payroll Corrections
Payroll Corrections is an all-encompassing phrase that considers all post-live check date changes that may need to occur for a payroll and that may also require amended returns. Some examples of payroll corrections are:
- Post Quarter-End Voids - payrolls that need to be voided after a given quarter has been closed and returns have already been filed
- Adding Historical Payrolls - payrolls that the company may not have provided during activation and/or processed outside of your payroll software
- State Jurisdiction Changes - An employee who may have a new workplace that was not updated when payroll was processed.
More examples and their explanations can be found in the Check Knowledge Base.
Requests for payroll corrections should be submitted as a support ticket using the Correct Payroll request type. Multiple options for the type of correction required will be displayed.
In the event that a payroll must be added to the record (e.g. a missed historical) Check support will provide a .csv template that contains all of the wage and tax fields customized to the company requesting a payroll correction. This is the same template used during company implementation and should be filled out with all applicable fields. Once it is returned to the Check Support team, it will be reviewed and added to the payroll record as required.
For all correction types, please be sure to include the check dates that need to be corrected, the nature of the correction, and all wage, tax, and benefit data required to make the change. Please also notify the Support team if the company consents to any necessary tax debits related to these corrections. This will minimize touch points between companies and ensure a smooth process.
Once corrections have been made, the Check team will process amended tax returns as needed and provide the relevant copies to the Partner to then provide to the company. Check will file the applicable returns with the tax agencies and these copies are for the company’s records.
The current SLA for payroll corrections is up to 20 business days depending on the correction request. These are manual requests and special care is required to append to the payroll record.
We understand that adjustments are often necessary for the current quarter's payroll. To ensure smooth processing and avoid the need for amendments, corrections should be submitted at least 20 business days before the quarter ends to make it in an original filing. It's worth noting that many corrections within the quarter can often be handled as voids or off-cycle payrolls. These adjustments can typically be made up until the quarter's end date.
If, for any reason, you miss the 20-day deadline, no worries! Corrections for that quarter will still be accepted and we will begin processing them starting from the first day of the month following the quarter's start. As an example, a Q1 Correction would be processed starting on May 1st. The reason these corrections don't start until the following month is because the initial filing needs to be completed first. This process aligns with the preferences of tax agencies and ensures that our original filing submissions are precise.
FEIN Failure
An FEIN ‘failure’ occurs after a company has been submitted to the Activation team for processing. The failure will sometimes be identified by the IRS’ EFTPS system quickly which allows the Activation team to request additional documentation, such as the SS-4 or a letter from the IRS with the company’s legal name and FEIN, before the company runs their first payroll. This is not always the case. The EFTPS system can take up to 10 business days to return a ‘terminated’ status and Check does not pause a company’s go-live date as a result of this delay.
If the failure occurs after the company has gone live, it will affect the tax payments submitted on behalf of the company to the IRS. The IRS will reject the payment submission causing a payment failure. When this occurs the Tax Operations team will immediately review the FEIN and verify that an SS-4 was not already received by the Risk team. If an SS-4 has not been provided, TaxOps will immediately notify the Partner via a Zendesk ticket and request the Partner/Company immediately provide a copy of the SS-4 or a letter from the IRS with the company’s legal name and FEIN.
The following timeline will apply to all companies with an FEIN failure:
- The first notification to the Partner/company will be issued once Check receives the notification of a failed IRS payment and identifying an SS-4 has not previously been provided.
- If the requested documentation is not provided within 5 business days, Check will reprompt the Partner/company a second time.
- An additional 5 business days will be given to provide the requested documentation.
- At the end of this 10 business day period, Check will have no choice but to block payroll until the requested documentation is provided.
- Finally, the ‘Applied For Tax IDs - Payment Processing’ process will be applied at the end of the quarter in question.
Early Filing Deadlines
Every state is different, and as a result, some states have different deadlines for the tax return due dates. When a tax return is due to an agency early in the filing month, it is considered an Early Filing. The earliest due date is the 15th with each due date cascading later and later, with the final due date typically being the last day of the month. In respect of these Early Filing Deadlines, it is important for the TaxOps team to adhere to the Quarter-End Deadlines.
Reconciliation Recap
The Reconciliation Recap is a summary of activity for each tax type and is included in the company tax returns that are loaded to the company documents each quarter. It will outline any credits due back to the company, additional collections needed from the company, refunds that will be issued by an agency, as well as any fractional amounts that were written off. Additionally, Check will write-off any variance amount that is less than $1.00 (positive or negative).
The top half of the Reconciliation Recap contains the following information:
- Fraction - The tax liability is only marginally different from the deposits and will be written off
- Deposit - Amounts to be collected
- Credit - Amounts to be refunded
- The net of the Deposit and Credit values equals the total Variance.
- Carry - Amounts carried forward to the next quarter, reducing tax owed to the agency
- Refund - An overpayment of taxes has occurred and will be refunded by the tax agency
The grid portion of the Reconciliation Recap contains the following detail:
- Tax Code - The tax code shown is a MasterTax tax code. The first two alpha characters will represent the applicable state.
- Description - A description of the MasterTax tax code and should assist in identifying the tax type that is represented.
- EIN - The Tax ID utilized for the applicable tax.
- Liability - A sum of the individual payrolls that were run over the course of the quarter.
- Prepaid - Tax payments that are assumed to be part of the history load completed during the implementation phase of the company’s life cycle. See Mid-Quarter Collections.
- Deposits - The amount that is owed to the agency. This can be different from the amount shown in the Liability column. Typically the difference will be due to a tax rate change that occurred during the quarter. If even one payroll was run with an incorrect tax rate, a different amount will be displayed in this column.
- Prior Adjustment - Adjustments made to previous quarters that affect the current quarter’s balancing.
- Variance - The difference between the Liability/Prepaid columns and the Deposits column. The sum of this column populates the summary in the top half of the Reconciliation Recap. If the sum of the Variance is less than $1.00 (positive or negative) Check will consider this to be a write-off.

Last updated on September 25, 2025