Payroll filings

When you run US payroll, you owe the government two things: the tax money (deposits) and the paperwork that reports it (returns, also called filings). This page covers the paperwork. Bokapsys works out every figure from the pay runs you have posted, builds the forms, and prepares the exact upload files the agencies accept. You then file them yourself through the agency’s own website or by post.

Caution

Bokapsys never sends anything to the IRS, the Social Security Administration (SSA) or any state. It prepares the figures, the forms and the upload files. You file and pay through the agency’s own service, then record in Bokapsys how and when you filed.

1. 1Post pay runs
2. 2Generate the form
3. 3Check the lines
4. 4Sign
5. 5File it yourself
6. 6Mark as filed

Every payroll filing follows the same path.

The forms at a glance

Form	What it is, in plain words	Covers	When it is due	What Bokapsys gives you	Where you file it
Form 941	The quarterly federal payroll return. It reports the wages you paid, the federal income tax you held back from employees, and the Social Security and Medicare tax (together called FICA) for the quarter.	One calendar quarter	The last day of the month after the quarter ends	A worksheet (PDF) of every line, with the balance due after your recorded deposits	IRS, on paper or through an IRS-authorised e-file provider. Tax owed is paid through EFTPS
Form 940	The yearly federal unemployment tax return. FUTA (Federal Unemployment Tax Act) tax is paid by the employer only, on the first $7,000 of each employee’s wages for the year.	One calendar year	31 January of the next year	A worksheet (PDF) with FUTA owed and FUTA already deposited	IRS, on paper or through an IRS-authorised e-file provider
W-2	The yearly wage statement for each employee: their pay and the taxes held back. One W-2 per employee.	One calendar year	31 January of the next year, both to the employee and to the SSA	One W-2 per employee (PDF), a W-3 summary, and the W-2 upload file in the SSA’s own format	SSA Business Services Online (upload), plus a copy to each employee
1095-C	The yearly statement of the health coverage an applicable large employer offered each full-time employee, with the 1094-C summary. Only needed if you are an applicable large employer (see below).	One calendar year	Copies to employees by early March; to the IRS by the end of March (moved off weekends and holidays)	One 1095-C per employee and the 1094-C	Copies to employees; the IRS on paper with the 1094-C, or through an approved transmitter
State quarterly wage report	The report your state’s unemployment agency wants each quarter: each employee’s wages and the part your state taxes for unemployment insurance (SUI, state unemployment insurance).	One calendar quarter	Usually the last day of the month after the quarter. Your state sets its own date	A CSV file with one row per employee, and a filing record you can mark as filed	Your state’s employer portal

When a due date falls on a weekend or a federal public holiday, Bokapsys moves it to the next working day, as the IRS does. For example, the Form 941 for July to September 2026 is shown as due on 2 November 2026, because 31 October 2026 is a Saturday.

For contractors, see Contractor 1099s.

Before you start

Gather and set up these first. A missing item is the most common reason a form or file cannot be built.

• You can see Tax → Filings. Your role must include the tax filing permissions; see Team and roles.
• Your pay runs for the period are posted. Only posted (or paid) pay runs are counted. A draft or calculated run counts for nothing. See Run payroll.
• The period has ended. You can build a 941 or a yearly form before the period ends to look at the figures, but it is a draft: anything paid after today is missing, and Bokapsys asks you to confirm before you sign or record it.
• A taxpayer is set up under Tax → Tax Setup → Taxpayers: your legal business name, address and full 9-digit EIN (Employer Identification Number, the federal tax ID the IRS gave your business). The Generate button stays greyed out until a taxpayer exists. See Tax setup.
• For the W-2 upload file: your Social Security BSO user ID saved on the taxpayer. BSO is the SSA’s Business Services Online website. You get the user ID when you register there.
• Every employee has a Social Security number and a full home address saved under Payroll → People.
• For the state wage report: a State unemployment (SUI) registration for the state under Tax → Tax Setup → Jurisdictions, with the unemployment rate and taxable wage base from the notice your state sent you.
• Your federal deposits for the period are recorded, with Record deposit on Tax → Deposits Due or Record payment in Tax → Tax Payments. A deposit you made but did not record is not subtracted, so the form will show it as still owed. See Deposits.

Where to find payroll filings

Open Tax → Filings. The page has tabs across the top:

Tab	What it shows
All Filings	Every form you have generated, with buttons Generate 941, Generate 940, W-2 batch, 1099 batch and 1095-C batch, plus the Send these to the government yourself panel with the W-2 file, the 1099 file and the state wage report
Payroll	Only payroll forms: 941, 940, W-2, W-3, corrections (941-X and W-2c), 1095-C and state wage reports. Buttons: Generate 941, Generate 940, W-2 batch, 1095-C batch
1099 Contractors	Contractor forms. See Contractor 1099s

Each row shows the Form, who it is For (on per-person forms), the Period, the State, the amount (Box 1 on per-person forms, or the balance due), the Due date (red when overdue), the Status (with an Overdue badge and the date it was filed, where those apply) and a View button. Click a row to open its filing page.

Prepare Form 941 for a quarter

1. Go to Tax → Filings and open the Payroll tab.
2. Click Generate 941. A window titled Generate Form 941 (quarterly) opens. It starts on the last quarter that has ended.
3. Check the two fields (see the table below) and click Generate.
4. You see Form 941 created and its filing page opens with status Ready to review. If Bokapsys found something to check, the message reads Form 941 created, but check it and says what.
5. Read the What this form says card line by line against your own payroll records. See the worked example below for what each line means.
6. Continue on Filing a return to sign it, file it with the IRS, pay any balance through EFTPS, and click Mark as filed.

Field	What it means	Required	Example	Where to find it
Tax year	The calendar year of the quarter	Yes	2026	The year of the pay dates you are reporting
Quarter	Which three months: Q1 (January to March), Q2 (April to June), Q3 (July to September) or Q4 (October to December)	Yes	Q3 (July to September)	Payroll counts by pay date, not by the period worked

If you pick a quarter that has not ended yet, the window warns that it can be built as a draft to check the figures but cannot be signed or filed until the quarter is over. The window also tells you the year of your most recent posted payroll, in case you picked the wrong year.

You can also start from the Tax Calendar: click Prepare on the quarter’s row and the window opens with that quarter already chosen.

Worked example: a Form 941

Suppose in Q3 2026 you had one employee, paid $15,000 in total. Bokapsys held back $1,200 of federal income tax. You recorded deposits of $3,000 for that quarter’s payroll. The form’s lines would read:

Line	What it means	Amount
Number of employees paid	People paid for a pay period that includes the 12th of the quarter’s last month (12 September here), as the IRS asks	1
Wages, tips and other compensation	Wages subject to federal income tax (after any pre-tax deductions such as a 401(k))	$15,000.00
Federal income tax withheld	Income tax you held back from paychecks	$1,200.00
Taxable social security wages	Wages subject to Social Security tax, up to the yearly limit per employee ($184,500 for 2026)	$15,000.00
Social security tax (employer + employee)	6.2% from the employee plus 6.2% from you = 12.4%	$1,860.00
Taxable Medicare wages and tips	All wages subject to Medicare tax (no limit)	$15,000.00
Medicare tax (employer + employee)	1.45% from the employee plus 1.45% from you = 2.9%	$435.00
Wages subject to Additional Medicare Tax	Only the part of an employee’s pay above $200,000 in the year (2026 figure)	$0.00
Total taxes after credits	The tax amounts added together	$3,495.00
Total deposits already made	Deposits you recorded for payroll in this quarter	$3,000.00
Balance due	What you still owe for the quarter	$495.00

If your recorded deposits are more than the total tax, Overpayment shows the difference instead.

The form also fills in Deposit schedule (line 16): whether you are a monthly or semi-weekly depositor and, for a monthly depositor, the tax for each month of the quarter. A semi-weekly depositor attaches Schedule B instead; see Deposits. If your tax was small enough that the IRS lets you pay it with the return rather than depositing it, the form says why.

A deposit counts toward the quarter of the payroll it covers, not the day you paid it. If you pay March’s tax on 15 April, it still counts on the Q1 form, as long as it is recorded against March. See Deposits.

How to check it worked

• The filing appears on the Payroll tab with the right period and a status of Ready to review.
• Wages on the form match the total gross wages of your posted pay runs for the quarter on Payroll reports (less any pre-tax deductions).
• Total deposits already made matches what you actually paid through EFTPS for that quarter, and Deposits on the return on the filing page shows the same figure.

Common problems

What you see	What it means	What to do
The Generate button is greyed out and the window says Add your business details under Tax Setup → Taxpayers before creating a filing.	No filing entity exists yet	Add one under Tax → Tax Setup → Taxpayers
All the lines are zero	No posted pay runs have a pay date in that quarter	Post the pay runs, or check you chose the right quarter and year
Balance due is the whole quarter’s tax even though you paid	Your deposits are not recorded, or are recorded against the wrong payroll	Record each deposit on Tax → Deposits Due, then generate again
Your payroll has changed since this was built on the filing page	A pay run in the quarter changed after the form was built	Click Rebuild it before you sign. If the form is already filed, File a correction instead
“A us_941 filing for this period already exists in status “signed”. Amend it instead of regenerating.”	You already signed or filed this quarter’s form	You can regenerate a form only while it is Ready to review. Once signed or filed, it can’t be replaced. See Corrections

You can click Generate 941 for the same quarter again at any time while the form is still Ready to review. Bokapsys updates the same filing with fresh figures rather than making a second one.

Prepare Form 940 for the year

1. Go to Tax → Filings → Payroll and click Generate 940.
2. Check Tax year (it defaults to last year). Click Generate.
3. You see Form 940 created and the filing page opens with status Ready to review. Check the lines (example below).
4. Continue on Filing a return.

Worked example: a Form 940

Two employees in 2026: Ana earned $30,000 and Ben earned $5,000. FUTA applies only to the first $7,000 of each person’s pay.

Line	What it means	Amount
Total payments to all employees	All wages paid in the year	$35,000.00
Payments over the $7,000 limit per employee	Ana’s pay above $7,000 ($23,000). Ben is under the limit	$23,000.00
Total taxable FUTA wages	$7,000 for Ana + $5,000 for Ben	$12,000.00
FUTA tax before adjustments	0.6% of taxable FUTA wages (the 2026 net rate after the usual state credit)	$72.00
Credit reduction	Extra tax for employers in states that owe the federal government. No states are listed for 2026 in Bokapsys, because the list is only announced in November	$0.00
FUTA tax already deposited	FUTA deposits you recorded for the year	$0.00
Balance due	What you still owe	$72.00

The form also shows which state you paid state unemployment tax in (MU when it was more than one state, which means you also need Schedule A of Form 940).

FUTA only has to be deposited during the year once what you owe passes $500. Below that it carries forward, and you pay what is left with the 940.

The 940 is due 31 January. The filing card also tells you that if you deposited all your FUTA on time, you have until 10 February.

Prepare W-2s and the Social Security file

A W-2 goes to each employee and to the SSA. The W-3 is a one-page summary of all your W-2s. When you upload the W-2 file to the SSA, the W-3 is inside it, so you don’t send a separate W-3.

1. Make sure every employee paid in the year has a Social Security number and a full home address under Payroll → People.
2. Go to Tax → Filings → Payroll and click W-2 batch.
3. Check Tax year (it defaults to last year) and click Generate.
4. A window shows the result, for example 12 W-2 forms created for 2025 with Every form is ready to review. If anyone was left out, it says so: Left out because no Social Security number is on file: …. Add the number under Payroll → People and click W-2 batch again. Click Done.
5. Open the All Filings tab. Each employee now has a W-2 row, plus one W-3 row. Click View on a W-2 and then Download form to get the PDF copy for that employee.
6. Scroll down to the panel Send these to the government yourself. Check Tax year shows the right year.
7. In the W-2s for Social Security box, read the line “N employees in this file.” If it lists problems (your business address missing, employees with no Social Security number or no home address, employees who were paid but have no W-2), fix those first.
8. Click Download W-2 file. Save it. Don’t open and re-save it in a word processor or spreadsheet: the SSA reads the file byte by byte, and resaving can break it. You can also download it with Download W-2 file on any W-2 or W-3 filing page.
9. Optional but recommended: check the file with the SSA’s free AccuWage tool, which the box mentions.
10. Click Open SSA Business Services Online (ssa.gov/bso).
11. On the SSA site: sign in (or register as an employer first), choose Submit or Resubmit Wage File, and upload the file. BSO checks it straight away and gives you a receipt number. Write it down.
12. Give each employee their own W-2 copy: print the PDF from step 5, or send it electronically if they have agreed to that.
13. Back in Bokapsys, sign each W-2 filing and record that you filed it. See Filing a return. Choose Uploaded the W-2 file to Social Security and enter the receipt number.

Re-running W-2 batch for the same year rebuilds each employee’s W-2 that is still Ready to review. A W-2 that is already signed or filed is left as it is, and the result window lists those employees. The W-2 boxes include each employee’s Box 12 amounts (for example retirement contributions and health savings account money) and one state line for each state that withheld their income tax.

What the W-2 file needs

Item	Why	Where to set it
Full 9-digit EIN	The SSA can’t accept a file built from the last four digits	Tax → Tax Setup → Taxpayers, edit the taxpayer, field Employer Identification Number
Social Security BSO user ID	The SSA uses it as your signature on the file	Same window, under For filing W-2s and 1099s yourself
Your business address	It goes into the file	Same window, under Address
Contact name, Contact phone, Contact email	Go into the file so the SSA can reach you	Same window
A full Social Security number and home address for each employee	The SSA rejects a W-2 without them	Payroll → People, the employee’s record
Generated W-2s for the year, for everyone paid	The file is built from them	Click W-2 batch first

Common problems with the W-2 file

Message	What to do
“Add your full 9-digit EIN under Tax Setup → Taxpayers. The government file cannot be built from the last four digits alone.”	Edit your taxpayer under Tax → Tax Setup → Taxpayers and type the whole EIN. It is stored encrypted and only the last four digits are shown afterwards
“Add your Social Security Business Services Online user ID under Tax Setup → Taxpayers…”	Fill in Social Security BSO user ID on the taxpayer
“Your business address is missing its …”	Complete the address on the taxpayer
“No W-2s have been generated for 2026 yet.”	Click W-2 batch for that year first
“A Social Security number is missing or not valid for …”	Add the full number for each named employee, run W-2 batch again, then download the file again
“The home address is incomplete for …”	Complete the employee’s address under Payroll → People and run W-2 batch again
“… was paid in 2026 but has no W-2.”	Run W-2 batch again so everyone paid has a W-2

Prepare 1095-C health coverage forms

If your business is an applicable large employer (it averaged 50 or more full-time employees, counting part-timers as full-time equivalents, in the previous year), you must give each full-time employee a Form 1095-C describing the health coverage you offered them, month by month, and send the forms to the IRS with a Form 1094-C summary.

Bokapsys builds them from the hours it measured and the coverage your employees were offered or enrolled in under Payroll → Benefits. Measure the year’s hours first on the ACA Tracking tab there. See Benefits.

1. Go to Tax → Filings → Payroll and click 1095-C batch. You can also click Create 1095-C forms for … on Payroll → Benefits → ACA Tracking.
2. Check Tax year (it defaults to last year).
3. Bokapsys decides whether you are an applicable large employer from the previous year’s measured hours. Only if Bokapsys has no hours for that year to work it out from, tick We are an applicable large employer: we averaged 50 or more full-time employees, including equivalents, in …. Your confirmation is recorded on the forms.
4. Click Generate. A window shows how many forms were created, for example 24 1095-C forms created for 2025, and names anyone who has no form and why. Click Done.
5. Each employee’s 1095-C and the 1094-C now appear on the Payroll tab. Open each, check it, sign it, give the employee their copy, and file with the IRS: on paper with the 1094-C, or by passing the figures to an approved transmitter, since sending them electronically needs the IRS system only approved transmitters can use. Paper is only allowed below the electronic filing threshold (see below). Then click Mark as filed. See Filing a return.

If Bokapsys can see that you were not an applicable large employer, or cannot work it out and you did not tick the box, it refuses and says why. Re-running the batch rebuilds the forms still Ready to review and leaves any already signed or filed as they are.

Prepare a state quarterly wage report

The State quarterly wage report box appears in the Send these to the government yourself panel once you have at least one active State unemployment (SUI) registration.

1. Go to Tax → Filings → All Filings and scroll to Send these to the government yourself.
2. Set Tax year.
3. In State quarterly wage report, choose the State and the Quarter. If the quarter has not ended, a note says its figures will keep changing until it does.
4. Read the summary: how many employees were paid in the quarter, the taxable wages, and the tax at your unemployment rate. Below that you see your state employer account number (the last four digits from the registration) and the number of employees at each month end, which most states ask for. A warning lists anyone without a Social Security number.
5. Click Download wage report. You get a CSV file with one row per employee and the columns SSN, Last Name, First Name, Middle Initial, Total Wages, Taxable Wages and Unemployment Tax.
6. Once the quarter is over, click Create filing record. You see Filing record created. The report now appears as a filing, so it shows on your calendar and you can sign it and mark it as filed. You can download the CSV again from that filing’s page with Download wage report.
7. Sign in to your state’s unemployment or employer portal. Most states let you upload a file; some want the figures typed in. Either way, the file has every number you need.
8. Pay the state unemployment tax in that same portal. It does not go to the IRS.
9. Back in Bokapsys, sign the filing and record it with Mark as filed, choosing Filed on a state website.

Taxable wages are each employee’s wages up to the state’s yearly wage base (the amount of each person’s pay the state taxes). Once an employee passes it during the year, only the part below it counts. The tax is taxable wages multiplied by your unemployment rate.

This is one general CSV, not a specific state’s own file layout. If your state’s portal insists on its own layout, use the figures in the file to fill it in.

Common problems with the state report

Message	What to do
“Register for US-TX unemployment tax in Tax Setup before building its quarterly report.”	Add a State unemployment (SUI) registration for that state under Tax → Tax Setup → Jurisdictions
“Add your US-TX unemployment rate and taxable wage base to that registration before building the report.”	Bokapsys won’t guess either figure. Edit the registration and enter both from your state’s annual rate notice
“A social security number is missing for …”	Add it under Payroll → People
Create filing record is greyed out	The quarter has not ended yet, or the report has a problem listed above it. Wait until the quarter is over, or fix the problem

How many returns you file: the electronic filing rule

On the filing page of a W-2, a W-2c, a 1099 or a 1095-C, the How to file this card shows an Electronic filing threshold note. The IRS requires you to file electronically once you file 10 or more information returns of all kinds combined in a calendar year (2026 figure). Information returns are forms like W-2s, 1099s and 1095-Cs. Bokapsys counts every such form you have generated for the year. If you are at 10 or more, the note turns red and says You must file this electronically. Filing on paper can bring a penalty for each return.

How it works

• Figures come only from posted pay runs, counted by pay date within the calendar year. Payroll taxes are always reported by calendar year, even if your company’s fiscal year starts in another month.
• The 941, the 940, the W-2s, the deposits page and Schedule B all use the same calculation, so the four quarterly 941s add up to the year’s W-2 totals.
• If you switched to Bokapsys part-way through the year and imported your earlier provider’s year-to-date figures, those are included in the W-2s and in the yearly wage limits. See Switching providers.
• Deposits are taken from payments you have recorded, matched to the payroll they cover.
• Nothing is sent anywhere until you upload or post it yourself.

Related

Filing a returnSign, file and mark a form as filed.

DepositsWhat you pay, and by when.

Contractor 1099s1099-NEC forms and the IRIS file.

CorrectionsWhat to do when a filed form is wrong.