When most accountants think about payroll software, they think of software that calculates withholding and produces paychecks. Payrollix does that, but the bigger value sits on the back end: every quarter and every January, the system files the returns those calculations roll up into.
You do not file Form 941, 940, W-2, W-3, 1099-NEC, or 1096. Payrollix does. Federal returns go directly to the IRS. State returns go to each state. You see the filed copy, the acknowledgment from the agency, and an archive that holds it all for the required retention period.
What runs automatically
Quarterly federal returns (Form 941) are prepared from the quarter's payroll runs, reconciled against the wages and tax withheld in the system, and transmitted to the IRS in batches before the quarterly deadline. Annual federal returns (Form 940 for FUTA) follow the same pattern in January.
Year-end forms — W-2s for employees, W-3 transmittal to the Social Security Administration, 1099-NECs for contractors, and 1096 to the IRS — are generated for every active client and transmitted by the January 31 deadline. State quarterly withholding and unemployment returns follow each state's own schedule.
What we need from you
For us to file on a client's behalf, three things have to be in place: a current EIN and state tax IDs on the client record, a deposit-schedule designation that matches the IRS's assignment, and a signed Form 8655 (Reporting Agent Authorization) along with any state agent authorizations the client's jurisdictions require. The onboarding packet captures all of these at once when a client signs up.
Beyond that, what you provide is the underlying payroll: timely runs each pay period with correct wages, deductions, and employees. If the payrolls are right, the returns are right.
What you see along the way
Every transmitted return shows up in the client's tax-filings list with a status — submitted, accepted, or rejected — and a timestamp. The acknowledgment ID returned by the IRS or the state is on the record. You can download the filed XML, the PDF copy of the return, and the agency acknowledgment from a 4-year archive.
If a return rejects, the system queues it for fix-and-retransmit. Most rejects are data issues that resolve without your involvement; if something needs action on your end (a missing or wrong identifier, for example), you get a specific message about what we need.
What you still do
Tax notices that arrive at the client — paper letters from the IRS or a state agency — are not part of the filing flow. They come from the agency directly, often weeks after a return is accepted, and they require a response. Tax notices have their own workflow in Payrollix: upload the notice, the system tracks the deadline, and we work the response with you.
Year-end review is the other moment that needs your attention. Before W-2s go out to employees and to the SSA, you review and approve them. Same with 1099-NECs. Those reviews are walkthroughs, not blank-page filings — the data is ready and you confirm.
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