Managed Payroll · Payroll Tax Filing Services

Payroll Tax Filing Services: Every Deposit, Return, and W-2 Filed On Time in All 50 States

A payroll tax deposit that lands 16 days late costs 10% of the deposit before interest. A quarter of unregistered state withholding costs a notice, back tax, and penalties months after the fact. BEG runs the deposit and filing calendar, reconciles every payment, files 941, 940, state withholding, unemployment, W-2 and 1099 returns under your EIN, and answers the notices, inside your existing platform or on isolved, at $25-$45 per employee per month.

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Outsourced payroll tax filing services for employers in all 50 states

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2%-15%IRS penalty on a late deposit
$25-$45Per employee per month, all-inclusive
3-5 DaysTo live managed payroll

TL;DR

Payroll tax filing is a calendar of deposits and returns with a penalty attached to every missed date, and the IRS holds the employer liable even when a third party files. BEG takes over the whole calendar: federal deposits on your assigned schedule, quarterly 941s, annual 940, state withholding and unemployment returns, local taxes, W-2s to the Social Security Administration, 1099s, and every notice that follows. It is included in managed payroll at $25 PEPM in your existing platform or $45 PEPM on isolved, with a $500 monthly minimum and no per-filing fees.

Where Payroll Tax Filing Goes Wrong

Why do payroll tax filings go wrong at growing companies?

Because the deposit schedule, the return calendar, and the state registrations all change as headcount grows, and nobody owns the calendar. The error surfaces as a penalty notice months later.

The person running payroll at a 40-person company is usually also running benefits, onboarding, and half of accounting. Tax filing is the task that gets done from memory, and memory is exactly what the IRS deposit rules punish.

Schedule
Your deposit schedule is assigned by the IRS and it moves
The IRS sets each employer as a monthly or semiweekly depositor based on the taxes reported in a lookback period, and a single day with $100,000 or more in accumulated liability forces a next-business-day deposit and flips you to semiweekly for the rest of the year and all of the next, per IRS Topic 757 on deposit requirements. Companies that grow through the $50,000 lookback threshold routinely keep depositing monthly for a quarter or two after they stopped being allowed to.
Penalty
Late deposits are penalized by the day, and the owner can be personally liable
The IRS failure to deposit penalty runs 2% of the deposit at 1-5 days late, 5% at 6-15 days, 10% past 15 days, and 15% if it is still unpaid 10 days after the first notice, with interest on top. Withheld income tax and the employee share of Social Security and Medicare are trust fund taxes, and the Trust Fund Recovery Penalty lets the IRS assess 100% of the unpaid trust fund amount personally against any responsible officer or owner.
Notices
The notice arrives long after the mistake, and someone has to answer it
A state unemployment rate notice that never gets keyed in, a withholding account opened in the wrong state, a 941 that does not tie to the deposits on Schedule B: none of these fail loudly. They surface as a letter with a balance due, a response deadline, and a penalty that has already been computed. Answering it correctly takes reconciled records, and the company that did not have time to file correctly rarely has time to reconstruct a year of deposits.

What BEG Files

What does a payroll tax filing service actually file?

Federal tax deposits on your assigned schedule, quarterly Form 941, annual Form 940, state withholding and unemployment returns, local income tax, W-2s to the Social Security Administration, and 1099s, plus the corrections and notices that follow.

Software calculates the tax. Someone still has to confirm the deposit schedule is current, tie the quarter to the deposits, key in the new state unemployment rate, and open the letter. That someone is the service.

Federal

  • Federal tax deposits through EFTPS on your monthly or semiweekly schedule
  • Form 941 each quarter, with Schedule B for semiweekly depositors
  • Form 940 and quarterly FUTA deposits once liability passes $500
  • Form W-2 and W-3 e-filed with the Social Security Administration
  • Form 1099-NEC and 1099-MISC for contractors, at the 2026 $2,000 threshold
  • Form W-2c and 941-X corrections when a prior period has to be fixed

State and local

  • State withholding registration, deposits, and returns in all 50 states
  • State unemployment insurance wage reports every quarter
  • New SUI rate notices applied the quarter they take effect
  • Local and municipal income tax where it exists
  • State annual reconciliations and state W-2 copies
  • New hire reporting in every state where you hire

All of it inside the $25-$45 PEPM managed payroll rate. No per-filing charge, no per-state charge, no year-end surcharge. A $500 monthly minimum applies. See the full scope on the managed payroll services overview.

The Part Most Providers Skip

Who is liable when a payroll service files your taxes?

You are. The IRS states that using a payroll service provider or reporting agent does not relieve the employer of its employment tax liability, which is why the provider you choose and the visibility you keep both matter.

The IRS is direct about this in its guidance on third party payer arrangements: a payroll service provider or reporting agent can prepare returns, file them, and make deposits under your EIN, but it does not assume any of the employer's employment tax liability. If the deposit does not arrive, the penalty is yours. The same guidance recommends that every employer using a third party enroll in EFTPS so it can see, under its own EIN, that the deposits actually posted.

BEG is built around that rule instead of against it. Filings run under your EIN and your address of record, so notices come to you and BEG answers them with you, rather than being routed to a provider mailbox you cannot see. Every deposit is reconciled against the payroll register and against EFTPS, and you keep EFTPS access to verify it yourself. When a provider tells you to stop worrying about payroll taxes, ask who receives the notice. When the answer is not you, that is a problem, not a feature.

Deposit Rules

How does the IRS decide when your payroll tax deposits are due?

By the total employment tax reported in a lookback period: $50,000 or less makes you a monthly depositor, more makes you semiweekly, and $100,000 accumulated on any single day is due the next business day.

SituationDeposit ruleWhere it breaks
$50,000 or less reported in the lookback periodMonthly depositor. Each month's liability is due by the 15th of the following month.Growth. The lookback is the four quarters ending June 30 of the prior year, so a company can cross the line without anyone recalculating.
More than $50,000 reported in the lookback periodSemiweekly depositor. Wednesday to Friday paydays are due the following Wednesday; Saturday to Tuesday paydays the following Friday.Off-cycle runs. A bonus or commission payroll on an unusual day creates a deposit date nobody put on the calendar.
$100,000 or more accumulated on any dayDue the next business day, and a monthly depositor becomes semiweekly for the rest of this year and all of next.Year-end bonuses. One large December run can trip the rule and quietly change the schedule for the following year.
Less than $2,500 in total tax for the quarterMay be paid with the quarterly Form 941 instead of deposited separately.The first hire. Employers that stay on this exception after passing it are late on every deposit of the quarter.

Rules summarized from IRS Topic 757 and IRS Notice 931, Deposit Requirements for Employment Taxes. Return due dates for Forms 941 and 940 are listed on the IRS employment tax due dates page. Form 940 reports FUTA tax at 6.0% on the first $7,000 of each employee's wages, reduced to 0.6% for employers that pay state unemployment tax on time, per IRS Topic 759.

The Math on One Late Deposit

Take a 50-person company with $3 million in annual wages. Federal withholding plus both halves of Social Security and Medicare runs roughly 27% of wages, about $31,000 per biweekly deposit, which makes the company a semiweekly depositor. One deposit that slips 16 days draws a 10% penalty, about $3,100, plus interest. That single miss costs more than a full month of BEG managed payroll at that headcount, which runs $1,250 to $2,250. A deposit that is never made, because the person who owned it left, exposes the owner personally to the trust fund portion, which is everything except the employer share of Social Security and Medicare, roughly 70% of the total in this example.

What a Scope Review Includes

BEG reads your current deposit schedule against your actual liability, your state registrations against where your employees sit, and your last four quarters of 941s against your deposits. Any gap is the deliverable. Live managed payroll runs 3-5 business days from signing, no migration required.

Year-End Filing

What does a payroll tax service handle at year end?

Reconciling four quarters of 941s to the W-2 totals, e-filing W-2s with the Social Security Administration and states, issuing 1099s, filing Form 940, and correcting anything that does not tie out before the deadline.

W-2 and W-3
W-2s go to employees and to the Social Security Administration by January 31, or the next business day when that falls on a weekend, per IRS Topic 752. Employers filing 10 or more information returns of any type in a year must file electronically. BEG reconciles the four quarterly 941s to the W-2 totals before anything is transmitted, because a W-2 that does not match the 941s is the most common trigger for an IRS or SSA mismatch letter the following summer.
1099-NEC and 1099-MISC
For payments made in 2026 and later, the reporting threshold for nonemployee compensation rose from $600 to $2,000, indexed for inflation after 2026, per the IRS instructions for Forms 1099-MISC and 1099-NEC. BEG tracks contractor payments through the year so the January filing is a review, not a reconstruction. Classification is checked first, since a contractor who should have been an employee is a payroll tax problem, not a 1099 problem. See payroll for 1099 contractors.
2026 wage bases and rates
Social Security tax applies to the first $184,500 of wages in 2026 at 6.2% for the employee and the employer, per the Social Security Administration contribution and benefit base. Medicare has no wage cap at 1.45% each side, and employers must withhold an additional 0.9% once an employee passes $200,000 in the year, per IRS Topic 751. These change every January and are a common source of over- and under-withholding in self-managed setups.
Form 940 and state unemployment
Form 940 is due January 31, with a February 10 extension for employers whose FUTA deposits were all made on time. Every state issues a new unemployment insurance rate for the coming year, usually between November and March, and a rate that is not keyed in means every quarterly wage report after it is wrong. BEG applies the new rate the quarter it takes effect and reconciles the state account when the notice arrives.

Free Tool

If you want to see the whole calendar before deciding whether to hand it off, the 2026 payroll tax calendar lists every federal deposit and return date on one page, including the quarterly 941 dates, the 940 deadline, and the W-2 and 1099 filing dates. Most companies that print it find at least one date they were handling from memory.

FAQ

Common questions about payroll tax filing services

What is a payroll tax filing service?

A service that calculates, deposits, and files an employer's federal, state, and local payroll taxes on the employer's behalf. That covers federal tax deposits, quarterly Form 941, annual Form 940, state withholding and unemployment returns, local taxes, year-end W-2s and 1099s, and the corrections and notices that follow. BEG delivers it as part of managed payroll rather than as a separate line item.

How much does outsourced payroll tax filing cost?

With BEG it is included in managed payroll at $25 per employee per month inside your existing platform or $45 per employee per month on isolved, with a $500 monthly minimum. There is no per-filing, per-state, or year-end charge. Providers that price tax filing as an add-on typically charge per return, which makes a multi-state company's bill grow with every registration.

Am I still liable if my payroll provider files late?

Yes. The IRS holds the employer responsible for deposits and returns even when a payroll service provider or reporting agent handles them. Some providers offer to cover penalties caused by their own error, which is worth having, but it is a contract promise, not a shift in legal liability. That is why BEG keeps filings under your EIN and address of record and recommends you keep EFTPS access to verify deposits yourself.

Do I have to switch payroll software to use BEG for tax filing?

No. At $25 PEPM, BEG runs payroll and tax filing inside the platform you already use. If you would rather move to isolved, the $45 PEPM rate includes the platform. Either way, live payroll runs 3-5 business days from signing, and there is no migration project. If you are mid-year, read how to switch payroll providers for who files the final returns with the old provider.

What happens if we already have a payroll tax notice or a missed deposit?

It gets handled as part of onboarding. BEG reconciles the periods in question, files or amends what is missing, and responds to the notice with the reconciled records. Penalty abatement is often available for a first-time failure with a clean prior history, and it has to be requested. See fixing payroll errors and penalties for how that process works.

Does BEG handle payroll taxes in every state?

Yes, in all 50 states and the District of Columbia, including local income taxes where they exist. Registration in a new state, withholding by work location, and reciprocity between states are covered on the multi-state payroll page. BEG is headquartered in Dallas-Fort Worth and delivers the service remotely nationwide.

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