Bookkeeping for S corporations: payroll, distributions and shareholder loans

Electing S corporation status changes how an owner gets paid, and the books have to change with it. Many new S corporations keep recording owner withdrawals as draws, which causes errors on the tax return. This guide covers the entries that matter.

By Muhammad Bilal, Chartered Accountant. Reviewed by Mirza Fahad Baig, Chartered Accountant. Checked against official sources on . 3 minute read.

Short answer

S corp bookkeeping differs from an LLC's in four places. The owner is paid a salary through payroll, recorded as wages with payroll taxes. Profit taken beyond salary is recorded as distributions, not draws. Loans between owner and company need documentation and their own accounts. And owner health insurance and reimbursements follow specific rules.

At a glance

Owner pay
Salary through payroll, with taxes
Extra profit taken
Distributions, not draws
Loans to the owner
Documented, with interest, or risk reclassification
Loans from the owner
A liability; may give debt basis
Owner health insurance
Paid by the company and added to W-2 wages
Owner expenses
Reimbursed under an accountable plan
Bookkeeping for S corporations: payroll, distributions and shareholder loansSteps: 1. Payroll liabilities clear; 2. No owner draws; 3. Loan balances agree; 4. Reimbursements documented.THE PROCESS AT A GLANCEBookkeeping for S corporations: payroll,distributions and shareholder loans1Payroll liabilitiesclearDeposits made on time2No owner drawsOwner withdrawals recorded asdistributions or loans3Loan balances agreeTo the loan agreements4ReimbursementsdocumentedUnder the accountable planChecked against official sourcesTax BakersBookkeeping for S corporations: payroll, distributions and shareholder loansSteps: 1. Payroll liabilities clear; 2. No owner draws; 3. Loan balances agree; 4. Reimbursements documented.THE PROCESS AT A GLANCEBookkeeping for S corporations:payroll, distributions andshareholder loans1Payroll liabilities clearDeposits made on time2No owner drawsOwner withdrawals recorded as distributionsor loans3Loan balances agreeTo the loan agreements4Reimbursements documentedUnder the accountable planChecked against official sourcesTax Bakers
The process at a glance: 1. Payroll liabilities clear; 2. No owner draws; 3. Loan balances agree; 4. Reimbursements documented.

Which accounts does an S corporation need?

AccountUsed for
Officer wagesThe owner's salary
Payroll tax expenseEmployer Social Security, Medicare and unemployment taxes
Payroll liabilitiesWithheld taxes not yet deposited
DistributionsProfit paid to shareholders, an equity account
Loan to shareholderMoney the company lent the owner, an asset
Loan from shareholderMoney the owner lent the company, a liability
Paid-in capital and retained earningsEquity

How is owner payroll recorded?

Each payroll records gross wages as officer wages, employee tax withholdings and employer payroll taxes as liabilities and expenses, and net pay from the bank. When the taxes are deposited, the liabilities clear. Payroll software usually posts these entries. See S corp owner payroll and reasonable salary.

Pay the salary regularly through the year.

How are distributions recorded?

Debit distributions and credit the bank. Distributions are not expenses and are not on the W-2. With more than one shareholder, distributions must be made in proportion to ownership, because S corporations can have only one class of stock. Personal costs paid from the company account are distributions too, unless repaid.

Distributions should not be paid unless the owner has already received a reasonable salary for the year, and are usually paid from profit already earned. Keep a running schedule of distributions by shareholder, which the tax preparer will need.

How are shareholder loans handled?

Money the company lends the owner should have a written note, a repayment schedule and interest at least at the IRS applicable federal rate; otherwise the IRS may treat it as a distribution or as wages. Money the owner lends the company is a liability; repayments of principal are not income. A direct loan from the shareholder gives debt basis, which can allow losses to be deducted. See contributions vs loans.

Record interest on shareholder loans as interest income or expense, and keep repayments on schedule; long-unpaid balances invite questions.

How is owner health insurance handled?

For a shareholder owning more than 2%, the company pays or reimburses the premiums, deducts them, and includes them in the owner's W-2 box 1 wages, but not in Social Security and Medicare wages. The owner can then claim the self-employed health insurance deduction. See the self-employed health insurance deduction.

How are owner expenses reimbursed?

Under an accountable plan: the owner submits receipts and a business purpose for business costs paid personally, such as a home office share or mileage, and the company reimburses them, tax-free to the owner and deductible to the company. Without a plan, reimbursements can become taxable wages.

Write the plan down, even as a short company resolution.

The rules are set out in accountable plans.

What should be checked each month?

  1. Payroll liabilities clear

    Deposits made on time.

  2. No owner draws

    Owner withdrawals recorded as distributions or loans.

  3. Loan balances agree

    To the loan agreements.

  4. Reimbursements documented

    Under the accountable plan.

What does a year look like?

A one-owner S corporation earns $150,000 before owner pay. The owner takes a $70,000 salary, on which the company pays about $5,355 of employer Social Security and Medicare tax plus a small amount of unemployment tax. The company also pays $9,000 of owner health insurance, added to the W-2. Profit after these costs, about $65,600, passes through on the K-1. The owner takes $50,000 of it as distributions, recorded in equity; the rest stays in the company.

What does the year end involve?

Add owner health insurance to the W-2, file payroll returns and Forms W-2, and prepare Form 1120-S with Schedules K-1. The return includes a balance sheet and reconciliations of book income and retained earnings, unless the company meets the small-company exceptions. Shareholders track their own stock and debt basis, attaching Form 7203 when required. See Form 1120-S and Forms W-2 and W-3.

Running an S corporation?

We run your owner payroll, record distributions and shareholder loans correctly, and prepare your Form 1120-S and K-1s.

Questions people ask

How is S corp bookkeeping different from an LLC's?

The owner is paid through payroll, extra profit is recorded as distributions, shareholder loans need documentation, and owner health insurance goes on the W-2.

Can an S corporation owner take draws?

Withdrawals are recorded as distributions, after a reasonable salary has been paid.

How do I record a loan from my S corporation?

As a loan to shareholder asset, with a written note, repayment schedule and interest at least at the applicable federal rate.

How is S corporation owner health insurance recorded?

Paid or reimbursed by the company, deducted, and included in the owner's W-2 box 1 wages.

Sources

Every fee, date and rule on this page was taken from these official and primary sources.

  1. IRS: S corporation compensation and medical insurance issues
  2. IRS: Instructions for Form 1120-S
  3. IRS: Applicable federal rates
  4. IRS: About Form 7203

Rules and fees change. If you are reading this long after October 1, 2026, confirm the figures with the source before you rely on them.

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This guide is general information. It is not tax or legal advice for your situation.