Know what the accounts should show
After a payroll run, the liability accounts hold employee withholding plus employer taxes not yet deposited. After a deposit, the balance drops by that amount. At quarter end, the balance should equal what you owe but have not yet deposited, which should be small or zero if you deposit promptly.
A balance that grows quarter after quarter means deposits are not being recorded properly or taxes are unpaid. Either one needs attention.
Gather three sets of documents
You need the payroll reports from your provider for the quarter, the deposit confirmations or bank statement lines for tax payments, and the filed quarterly returns. If the provider files for you, download the filing confirmations. The three sets should tell the same story.
Print or save a payroll summary by tax type. It lists gross wages, withholding and employer taxes, which you will compare to the books.
Compare wages and taxes to the books
Total wages in the payroll summary should equal wage expense in the profit and loss for the same period. Employer tax totals should match payroll tax expense. If your books record wages from bank payments instead of payroll reports, differences often point to missing accruals or to a wrong date.
Pay special attention to the last payroll in a quarter. A payday on the first of the next month, for work in the old quarter, belongs on the right side of the line for filings but may be recorded differently in the books.
Trace each deposit
List every tax payment from the bank statement. Each should clear a matching liability. Common issues: a deposit recorded as an expense instead of reducing the liability, a penalty or interest charge lumped in with the tax, and deposits made by the provider but never recorded in the books.
Separate penalties and interest into their own account. They are not ordinary tax, and your preparer treats them differently.
Resolve differences and document
If the liability balance is off, find the transactions responsible rather than plugging the difference. Correct entries in the books and write a note describing what happened. Save the reconciliation with the payroll reports for the quarter.
If you discover that a filing or deposit was missed, bring it to your payroll provider or CPA straight away. Early correction is usually cheaper.
A simple worksheet layout
Make a sheet with one row per tax type and four columns: opening balance, added by payroll runs, paid by deposits, and ending balance. Fill it from the payroll reports and bank statement, then compare the ending balance to the liability account in your books. Any row that does not agree gets investigated before moving on.
Keep one sheet for each quarter. After a year you will have four, and a quick look across them shows any account whose balance keeps creeping up.
Common questions
How often should I do this?
Quarterly at minimum, and monthly if payroll is large or you have had errors. It pairs well with your regular month-end close.
My provider says everything is filed. Do I still need to reconcile?
Yes. The provider's records and your books can differ in timing or posting. Reconciling shows whether your books reflect reality.
What if there are unfamiliar liability accounts?
Ask your provider what they represent. Some are benefit deductions, garnishments or state programs.
This guide is general information, not tax, legal or accounting advice. Rules, fees and due dates change; check with the IRS, the NJ Division of Taxation or a licensed professional for your situation.