Quarter End Preparation Guide

• ✅ Clear filing and payment blockers: prior failed filings, missing tax IDs, unresolved NSFs

• ✅ Review and explain balancing payrolls and upcoming variance collections/refunds

• ✅ Confirm where Check intends to file and whether the customer wants us to file there

• ✅ Ensure complete payroll history is loaded (especially prior provider history)

• ✅ Terminate churned customers and check in on inactive accounts

1. Resolve tax filing and payment blockers

• Missing Tax Inputs Report: Missing or incorrect tax IDs prevent Check from filing or paying taxes on time. These gaps are the most common cause of delays and rejections.

“Your account is missing required state or local tax IDs. Please update these as soon as possible so we can file on your behalf without delays. Without this required information, you may be responsible for agency assessed penalties or interest.”

• Funding Failures: Check will not file and cannot guarantee on-time tax remittance until the account balance is resolved. Check will still generate employer tax return copies, but they will not be filed with the agency.

“Your account currently has an unresolved funding failure. We’re unable to file or guarantee on-time tax payment until this is corrected. If not resolved before the end of the quarter, you may be responsible for agency assessed penalties or interest.”

• Failed Filings: Review both the prior quarter’s failed filings and the current quarter’s proactively detected failures. Unresolved failures from the prior quarter often predict issues this quarter, usually caused by missing tax IDs, incomplete TPAs, or inactive accounts. In addition, Check flags expected failures for the upcoming quarter based on known missing requirements. If these issues aren’t corrected before filing month, customers may face late filing penalties and delayed submissions.

“We were unable to complete one or more of your tax filings last quarter due to missing or incorrect information. This issue may cause delays again this quarter. Please address the outstanding items so we can submit your upcoming filings on time and help you avoid agency-assessed penalties or interest.”

• Employers Starting This Quarter: New employers can generate already-filed errors if they haven’t fully terminated services with their prior provider. This results in duplicate filings and rejected returns. Customers must confirm termination and ensure their last filing date is set correctly.

“To avoid duplicate or rejected tax filings, please confirm that you’ve fully terminated filing services with your previous provider and set your last filing date appropriately. This ensures filings for this quarter are submitted correctly and without delays.”

• Missing or Invalid SSNs: Incorrect or placeholder SSNs require amendments later and may impact employees’ access to state or federal benefits. Correcting these now prevents filing errors, mismatches, and downstream employee issues.

“We identified one or more employees with missing or invalid Social Security numbers. Please update these as soon as possible to ensure accurate reporting and to prevent issues for employees who may need to access state or federal programs.”

2. Get ahead of quarter-end refunds or collections

Beginning in Q4 2025, in addition to the “regular” and “off cycle” payrolls that are created as companies are running payroll, you will see a special type of payroll called “balancing” payrolls.

Throughout the quarter, Check maintains a draft balancing payroll for every company with a payday set to the last day of the quarter. This balancing payroll gives you an early signal of any upcoming tax liability adjustments that may result in a variance collection or refund. It recalculates taxes across the quarter to ensure taxable wages and amounts align with agency rules for filing, and it updates weekly as payroll history changes.

This is a standard process in the payroll industry—taxes can fall out of balance for many reasons, such as a mid-quarter rate change or simple rounding drift over time.

Reviewing balancing payrolls across companies

Draft balancing payrolls are available for preview in the Quarterly Variance Report in Console. You can access the report by first navigating to the Reports tab in Console, selecting “Quarterly variance report”, and then selecting the current year and quarter.

Example CSV

Company ID	Company Legal Name	Total Liability	Balancing Payroll	Updated At	Approved At	Payment	Payment Type	Payment Date	Payment Amount	Agency Refund Amount
com_GLNmgeXia8yioT968nSc	Stark Industries	295.12	pay_st1wudRlzHua3EzFqMRA	2025-11-19T15:38:00Z	2026-01-02T09:24:00Z	pyt_HlSYFp9q8DhUhSIbJju6	Collection	2025-01-05	295.12	0.00
com_EaDebPPxqR4oZHzflpQ5	Oscorp	125.60	pay_gQcrWL4dRWIm6jDjZI6j	2025-11-19T15:38:00Z	2026-01-02T09:24:00Z	pyt_zfJaAyXnjOicFpLBnWIG	Refund	2025-01-05	75.20	50.40

The Quarterly Variance Report shows all draft balancing payrolls across companies, as well as payment amounts after the quarter is closed and balancing payrolls are approved. The most important attributes to review are:

• Total liability — the net tax liability amount from the balancing payroll.

• Payment amount — the expected employer refund or collection amount from Check.

• Agency refund amount — the expected refund that the employer will receive from the agency after filing is completed.

The resulting transaction or pay adjustment can differ from the overall liability adjustment when funds have already been sent to the agency and cannot be refunded directly to the employer.

• If Check still holds the funds for a given tax and they exceed the amount due, Check can refund the employer.

• If Check no longer holds the funds, the amount will be over-reported on the return so that the agency can process a refund.

Reviewing balancing payrolls for a single company

To dig deeper into the root cause of tax variance adjustments, you can preview draft balancing payrolls at the company level. This will return a breakdown of tax variances on a company’s balancing payroll by employee and by tax.

To do this, first navigate to the balancing payroll in Console (which you can do by searching for the payroll ID in the search bar, or by navigating to Payrolls for the company and selecting the balancing payroll for the quarter). Then, open the “…” menu in the upper right and select Export payroll journal.

Example CSV

Last Name	First Name	Period Start	Period End	Payday	Payment Method	Gross Total	Net Pay	Social Security Tax (EE)
Stark	Tony	2025-10-01	2025-12-31	2025-12-31	Manual	0.00	-0.01	0.01
		2025-10-01	2025-12-31	2025-12-31	0	0.00	-0.01	0.01

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If you wanted to expose this balancing payroll preview directly to employers in your platform, you can use the preview a payroll API endpoint on the balancing payroll.

Understanding the root cause of tax variances

There is not always a straightforward answer to “why” tax variances exist for a company. A few example causes of tax variances are:

• Mid-quarter rate changes — For example, if a company’s state unemployment rate changes mid-quarter, then payrolls that were calculated during the quarter before the rate change was entered in Check will produce a variance.

• Exemptions added or removed — If an exemption to a tax was added or removed mid-quarter, then payrolls that were already processed may produce a variance to retroactively add or remove the tax.

• Mistakes during company setup — A company’s historical payrolls may have been entered with incorrect subject wages or tax amounts.

• Rounding throughout the quarter — Simple rounding differences between calculating a tax payroll by payroll vs. in aggregate on the entire quarter may produce minor variances.

• Other agency-imposed requirements — For example, credit reduction states for FUTA are announced in November ever year, and will appear as tax variances for employers in the affected states in Q4.

The best way to begin investigating the root cause of tax variances for a company is to start with payroll summary and payroll journal, which can be accessed from the Company > Reports tab. Select the option to “Include taxable wages” in the report.

Once you have the reports, look for any instances where the calculated tax amount does not equal the taxable wages times the rate for the tax. Those are more than likely the source of the tax variance, and may help you identify one of the root causes above.

Using draft balancing payrolls proactively

• For large expected variances, communicate early. Proactively notify employers well in advance of Quarter End. A good example is the FUTA Credit Reduction at Q4 Quarter End.

• If the balancing preview looks wrong, escalate quickly. If you have identified the root cause of tax variances and believe that corrections are required, create a Support request with the “Corrections + Amendments” request category. Addressing it early increases the chances it can be resolved before filings.

“Your estimated quarter-end variance [collection or refund] is $X. This amount will be finalized after quarter-close. If you see anything that looks unexpected—such as a large change in taxable wages or state tax amounts—please let us know. We can pause or adjust the timing while we review the details together before the amount is finalized.

3. File only where expected to file

4. Correct missing or inaccurate payroll history

• For employers who migrated this quarter, confirm no payrolls were skipped during onboarding and check for obvious gaps (e.g., first payroll mid-quarter with no prior history imported).

• Ask customers to notify you of any missed or off-system/off-cycle payments that haven’t flowed through the platform.

• Ensure any needed payroll corrections or adjustments are submitted well before quarter-end (ideally **20 business days).

• Review any failed payrolls that have not been voided as these can be a source of unfunded tax payments or overstating taxes owed.

“Review your quarter’s payroll history for completeness. If you processed any payroll outside of our platform this quarter (including with a prior provider), please let us know and provide wage/tax details. This helps ensure your filings are complete and avoids amended returns later.”