Payroll in your books

Payroll is part of your bookkeeping, not a separate system. When you post a pay run, Bokapsys records it in your general ledger (the complete record of every amount in every account), so your Income Statement, Balance Sheet and Trial Balance include it automatically. This page explains exactly what is recorded, in which accounts, and how the amounts you owe are cleared when you pay them.

1Post the pay run
2Wages and taxes recorded
3Pay employees
4Pay the tax
5Liabilities back to zero

Words used on this page

Word	What it means
Debit / credit	The two sides of every bookkeeping entry. They always add up to the same total. An expense goes up with a debit; an amount you owe goes up with a credit.
Expense	A cost of running your business. Shown on the Income Statement.
Liability	Money you owe someone. Shown on the Balance Sheet.
Accrued	Owed but not yet paid.
Control account	An account Bokapsys posts to automatically for a particular purpose, such as wages.
Period	A month in your books. A closed period can’t be posted to.

When payroll reaches your books

Pay run step	Effect on your books
Draft, calculate, review, approved	Nothing. You can create and check as many runs as you like.
Post to GL	Wages, employer taxes and benefits are recorded as expenses; taxes, deductions and net pay as amounts you owe. Dated the pay date.
Record payment	Net pay owed to employees is cleared against the bank account you chose in Paid from. Dated the Paid on date you entered.
Reverse (posted runs only)	Opposite entries for everything the run posted, dated the day you reverse. A run that has been recorded as paid can’t be reversed.
Record payment on a tax payment (in Tax)	Payroll tax owed is cleared against your bank account, on the date you say you paid.

Posting needs the month of the pay date to be open. If it is closed you see Cannot post payroll: period YYYY-MM is closed. and nothing is recorded. The same applies to Record payment (the month of the paid-on date), to reversing (the current month) and to recording a tax payment.

The accounts payroll uses

Bokapsys posts payroll to these accounts from the standard chart of accounts. They sit under Salary, Wages & Benefits (expenses) and Accrued Compensation (liabilities).

What is recorded	Account	Side when posting
Earnings: salary, hourly pay, overtime	6010 Salaries & Wages	Debit (expense)
Employer taxes: your Social Security, Medicare, FUTA, state unemployment	6032 Payroll Taxes - Employer	Debit (expense)
Employer benefit contributions (your share of a plan)	6020 Employee Benefits	Debit (expense)
Taxable non-cash benefits (imputed income)	6025 Employee Benefits - Other	Debit (expense)
Reimbursements paid through payroll	6040 Other Personnel Related	Debit (expense)
Net pay you owe employees	2101 Accrued Employee Payroll	Credit (liability)
Taxes withheld from employees plus employer taxes, all owed to the government	2103 Accrued Payroll Taxes	Credit (liability)
Employee deductions you owe to others: benefit premiums, 401(k), HSA/FSA, garnishments	2108 Payroll Clearing	Credit (liability)
Employer benefit contributions you owe to providers	2102 Accrued Employee Benefits	Credit (liability)
Money leaving your bank when you record a payment	The bank account you choose in Paid from	Credit

Each posted line is described like Payroll PR-00001 - Salaries & Wages, and the payment lines like Payroll PR-00001 disbursement - ….

Changing the accounts

The bank account is chosen each time you record a payment, from the cash accounts in your chart of accounts. Every bank account you add under Company settings has one. See Chart of accounts.
Pay items of your own can each post to an account you choose, in the item’s Account field. Leave it on Default payroll account to use the accounts in the table above. See Compensation.
The standard payroll accounts in the table above can’t be changed from the app. If your business needs payroll to post elsewhere, contact Bokapsys support. See Contact.
Don’t delete or rename those accounts in your chart of accounts. If one is missing when you post, posting stops with a message such as Account 6010 is not in this workspace’s chart of accounts or Payroll control account “…” is not configured, and nothing is recorded. Restore the account and post again. (The message mentions Company settings; the accounts are not set there.)

Worked example

Maria’s pay run PR-00001 (from Run payroll): $2,000.00 gross, $309.15 employee taxes, $219.00 employer taxes, $1,690.85 net, pay date 19 June 2026.

1. You click Post to GL. Recorded on 19 June 2026:

Account	Debit	Credit
6010 Salaries & Wages	2,000.00
6032 Payroll Taxes - Employer	219.00
2103 Accrued Payroll Taxes (employee taxes 309.15 + employer taxes 219.00)		528.15
2101 Accrued Employee Payroll		1,690.85
Total	2,219.00	2,219.00

Your Income Statement now shows $2,219.00 of payroll cost for June. Your Balance Sheet shows $2,219.00 owed: $1,690.85 to Maria and $528.15 in taxes.

2. You upload the bank file, the bank pays Maria, and you click Record payment with Paid on 19 June 2026 and Paid from your operating account. Recorded on 19 June 2026:

Account	Debit	Credit
2101 Accrued Employee Payroll	1,690.85
Your operating bank account		1,690.85

3. You pay the federal deposit through EFTPS and record it in Tax. The federal part is the income tax withheld ($156.15) plus both halves of Social Security ($248.00) and Medicare ($58.00): $462.30. Recorded on the day you paid:

Account	Debit	Credit
2103 Accrued Payroll Taxes	462.30
Your operating bank account		462.30

4. What is left. 2103 still holds $66.00: FUTA ($12.00) and state unemployment ($54.00). They clear when you pay those and record the payments the same way. See Deposits and Tax payments.

Clearing what you owe

Net pay (2101)

Choose one way to record the money leaving your bank for net pay:

Either click Record payment on the run (step 2 above),
or let the withdrawal arrive from your bank feed or bank file upload and classify it to 2101 Accrued Employee Payroll. See Mapping statements.

Payroll taxes (2103)

Record each tax payment in Tax → Payments with Record payment. It debits 2103 Accrued Payroll Taxes and credits the bank account you paid from, on the date you paid. The same double-counting rule applies: if the EFTPS withdrawal also arrives from your bank, record it only once. See Tax payments.

Deductions and employer benefits (2108 and 2102)

Bokapsys does not pay your benefit providers, retirement plan or garnishment agencies. When you pay them, record the payment against 2108 Payroll Clearing (employee deductions) and 2102 Accrued Employee Benefits (your contributions), for example by classifying the bank payment to that account, or with a journal entry. Once everything is paid, both accounts return to zero for the period.

How it shows in your reports

Income Statement: payroll costs appear under Salary, Wages & Benefits, in the month of each run’s pay date.
Balance Sheet: amounts still owed appear under Accrued Compensation. A balance that keeps growing in 2103 means taxes recorded but not yet paid (or paid but not recorded).
Trial Balance and General Ledger: every payroll line is there with its description. See General Ledger and Financial reports.
Dashboard: payroll cost is included in your expenses. See Dashboard.

How to check it worked

Open Accounting → General Ledger and filter to the pay date.
Find the lines described Payroll PR-00001 - …. The debits equal the credits.
Check that 6010 Salaries & Wages for the run equals the run’s Gross (plus any reimbursements in 6040).
At month end, check that 2101 Accrued Employee Payroll is zero once everyone is paid, and that 2103 Accrued Payroll Taxes equals only the taxes not yet due or paid.

Common problems

Problem	Cause	Fix
Payroll is missing from the Income Statement.	The run is approved but not posted.	Click Post to GL.
Cash is lower than the bank by exactly the net pay.	Net pay recorded twice: Record payment and the bank statement.	Correct it with a journal entry: debit your bank account and credit 2101 Accrued Employee Payroll for the net pay. Ask your accountant if unsure.
2101 has a balance that never clears.	The run was paid but never recorded as paid.	Click Record payment, or classify the bank withdrawal to 2101.
A reversed run still shows in June.	The reversal is dated the day you reversed it.	Expected. The run and its reversal net to zero across the two dates.
Cannot post payroll: period … is closed.	The pay date’s month is closed.	Reopen the month, then post.

Run payrollPosting, paying and reversing a run.

Tax paymentsRecord payroll tax payments.

Chart of accountsYour accounts and control accounts.

ReconciliationProve your bank balance matches your books.