Payroll Deadlines for Small Businesses: What Happens Each Pay Run, Quarter and Year

What happens at every pay run

Every pay run has a few steps that happen in order. First the hours or salary get checked. Then the pay gets figured out. Then the right amounts get taken out for taxes and other items. Then the pay checks go out on the pay date.

A pay run is not just one number. It is a set of numbers. There is the gross pay, which is what the worker earned. There are the amounts taken out, which go to the agencies and other places. There is the net pay, which is what the worker takes home. Each of these needs to land in the right line in the books.

The pay date is the day the cash leaves the bank. The work that earned the pay happened before that day. The gap between the work and the pay date is normal. It gives whoever runs the payroll time to check the hours and fix mistakes.

Your CPA decides the accounting method and we keep the books consistent with it. The books should show the pay on the day the cash moves, or on the day your CPA tells you to use. The point is to pick one way and stay with it so the books and the bank agree.

What usually happens every quarter

Most payroll has a set of reports and payments that come due every three months. These are called quarterly reports. The quarters usually end in March, June, September and December. The reports and payments for a quarter are usually due in the month after the quarter ends.

A quarterly report sums up what you paid in that quarter. It shows the wages, the taxes taken out, and the amounts you owe. Some of these amounts get paid with the report. Some were already paid during the quarter and the report just confirms them.

The exact forms and dates depend on your state and your setup. Some businesses pay tax deposits during the quarter, then file a report that sums it up. Others file and pay at the same time. The rules are not the same everywhere.

Dates and rules change. Confirm the exact dates and forms with your payroll provider, your CPA, or the agency. Do not guess. A wrong date is as bad as a missed date.

Here is what a quarter usually holds.

• Wages paid in the quarter.
• Taxes taken out of the pay.
• Tax deposits sent during the quarter.
• A quarterly report that sums it all up.
• Any balance still owed with the report.

What usually happens at year end

At year end there is one more set of forms. These go to the people who worked for you and to the agencies. The two most common are W2 forms and 1099 NEC forms.

A W2 goes to each employee. It sums up their wages and the taxes taken out for the whole year. A 1099 NEC form goes to each contractor you paid. It shows what you paid them for the year. The two forms are not the same. An employee gets a W2. A contractor gets a 1099 NEC.

These forms are usually due by the end of January. That means copies go to the workers and copies go to the agencies around the same time. The exact date can shift when it lands on a weekend or a holiday.

Year end is also when the books get closed for the year. The payroll lines for the year should already match the pay records and the bank. If each pay run and each quarter was tied out, the year end close is just a sum. If they were not, the close turns into a hunt for the gap.

Dates and rules change. Confirm the exact due dates with your payroll provider, your CPA, or the agency. The end of January is the common window, but it is not a fixed rule.

Why late filings cause trouble

A late filing is a filing that misses its date. The trouble it causes comes in a few forms. None of them are good for the books.

First, the agencies can add a penalty. The penalty is not a fixed number. It can grow the longer the filing is late. Ask your payroll provider or your CPA what applies to you.

Second, a late filing can make the books and the agencies disagree. The books show one wage total. The agency record shows another. Finding the gap takes time and can hold up the month close or the year end close.

Third, a late filing can shake the trust of your team. Workers count on their pay and their forms being right and on time. A late W2 can slow their own tax work. A late pay run can slow their rent or their bills.

A simple calendar helps. Put every pay date, every quarter end, and every year end form on one calendar. Set a reminder a few days before each one. Then the dates do not sneak up on you.

How your books should show each payment and filing

The books should show payroll the same way every time. Each pay run adds a wage line. Each amount taken out goes where it belongs. Each filing gets recorded. When the cash leaves the bank, the books show it on the same day your CPA tells you to use.

This is the clean tie to your books. Payroll does not sit in a separate place. It lives in the same books as everything else. When the month closes, the payroll lines match the pay records and the bank. When the quarter closes, the quarterly report matches the sum of the pay runs. When the year closes, the W2 and 1099 NEC totals match the year of pay runs.

Your CPA decides the accounting method and we keep the books consistent with it. The books are the home base. The reports and the forms are sums pulled from the books. When the books are clean, the sums come out right.

We are QuickBooks Online Accountants, or QBOA, and we work in QuickBooks Online and Xero. We keep the payroll lines in the same software your books live in.

Made up example for teaching

A landscaping company with six employees

A landscaping company has six employees. Some are hourly and some are salaried. The owner runs payroll every two weeks. Each run has a pay date on a Friday.

The owner uses their own payroll provider. The provider figures out the pay, takes out the right amounts, sends the pay checks, and sends the filings. The owner does not run the pay by hand.

We keep the books. Each pay run shows up as a wage line. The amounts taken out go to the right lines. When the cash leaves the bank on Friday, the books show it on the same day the owner's CPA tells them to use.

At the end of each quarter, the owner's payroll provider files the quarterly report. The books already hold the sum of the pay runs for the quarter, so the report and the books agree. At year end, the provider sends out the W2 forms. The books already hold the year of pay runs, so the W2 totals and the books agree.

If a pay run had been missed in the books, the quarterly report and the books would not agree. The owner would have to find the gap before the close. Because each run was tied out as it went, the close is just a sum.

This is a made up example for teaching. Your numbers and your setup are your own. Confirm the dates and rules that apply to you with your payroll provider, your CPA, or the agency.

Common questions

What payroll deadlines do I need to track? You need to track three layers. Each pay run has a pay date. Each quarter has reports and payments. Each year has W2 and 1099 NEC forms, usually due by the end of January. Put all of them on one calendar.

When are W2 and 1099 NEC forms due? They are usually due by the end of January. The exact date can shift when it lands on a weekend or a holiday. Confirm the exact date with your payroll provider, your CPA, or the agency.

What happens if a filing is late? A late filing can add a penalty, make the books and the agencies disagree, and slow your team. The penalty is not a fixed number. Ask your payroll provider or your CPA what applies to you.

Do you run the payroll? Your CPA decides the accounting method and we keep the books consistent with it. We offer monthly payroll with pay runs every pay period, pay checks, filings and a clean tie to your books. You can read more on our payroll page or reach us on our contact page.