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How to connect Gusto to QuickBooks Online

Payroll runs in Gusto, the books live in QuickBooks. Here’s how to connect them, the accounts you need, and the one step that keeps payroll from showing up twice.

Shanin Drucquer

Shanin DrucquerGusto user since 2024 · Updated October 2026

Have these ready

  • Admin access in both Gusto and QuickBooks Online
  • The date you last closed your books (your cutover date)
  • Your accountant’s preferences for payroll accounts, if you have one
  • Any other way payroll gets into QuickBooks today, so you can turn it off

  1. Step 1 of 7 · 3 min

    Decide: sync, or bank feed only

    The sync posts a detailed journal entry for every payroll, with gross wages, employer taxes, and what you owe for benefits and withholdings in their own accounts. The bank feed is simpler: you categorize Gusto’s withdrawals as they show up. The sync gives your accountant the full picture; the bank feed gets you the totals.

    From Shanin

    I use the bank feed: net pay goes to wages and the tax withdrawal goes to payroll tax expense. When I tried the sync, payroll showed up twice. That usually means the bank transactions were added on top of the synced entries instead of matched to them, which step 6 covers. If you choose the bank feed, skip to the bank-feed section below.

  2. Step 2 of 7 · 8 min

    Connect, then set your sync preferences

    In Gusto, open the App directory, search for QuickBooks Online, click Connect, sign in to QuickBooks, and click Authorize. You need admin access in both. Gusto then suggests settings: the entry date, whether employer taxes are combined into one line, and how contractor payments are grouped.

    Choose the debit date for entries: it’s the day money leaves your account, so entries line up with your bank feed. Auto-sync is a switch in the Manage tab; keep it off until your first few entries check out.

    Gusto

    Sync settings

    Manage

    Entry date

    Debit date

    Employer taxes

    List each tax separately

    Auto-sync

    Off for now

    Save and continue

    Screens are recreated with example data.

  3. Step 3 of 7 · 10 min

    Create your payroll accounts in QuickBooks

    Gusto maps payroll to accounts in your QuickBooks chart of accounts, so set these up first. Use your accountant’s names if they have a preference.

    Accounts most small businesses need

    • Expense: Wages & Salaries (gross pay, including employee taxes withheld)
    • Expense: Employer Payroll Taxes (Social Security, Medicare, unemployment)
    • Expense: Employer Benefits, if you contribute to benefits
    • Liability: Payroll Liabilities, with sub-accounts for 401(k) and health insurance withheld
    • Bank: the checking account Gusto withdraws from
    QuickBooks

    Chart of accounts

    Payroll

    • 6000 Wages & SalariesExpense
    • 6010 Employer Payroll TaxesExpense
    • 2100 Payroll LiabilitiesLiability
    • 1000 Business CheckingBank

  4. Step 4 of 7 · 8 min

    Map every Gusto category to an account

    Back in Gusto, match each payroll category to one of those accounts. Every category needs a mapping, even ones you don’t use yet. If an account is missing, create it in QuickBooks, then click Refresh accounts in Gusto.

    Typical mapping

    • Wages & Salaries → Wages & Salaries (expense)
    • Employer Taxes → Employer Payroll Taxes (expense)
    • Employer Benefit Expense → Employer Benefits (expense)
    • Benefit and deduction liabilities → Payroll Liabilities sub-accounts
    • Net Pay and Taxes Paid → your checking account

    Watch out

    Unmapped categories stop the sync. Set default mappings, on the Default tab, so new earning types, deductions, or benefits map themselves.

    Gusto

    Account mapping

    Detailed

    Wages & Salaries

    6000 Wages & Salaries

    Employer Taxes

    6010 Employer Payroll Taxes

    Net Pay

    1000 Business Checking

    Save and continue

  5. Step 5 of 7 · 3 min

    Sync only payrolls after your cutover date

    Gusto offers to create entries for payrolls you’ve already run this year. Only sync payrolls after the date you last closed your books, and only ones that aren’t already recorded.

    Watch out

    Payrolls you already categorized from the bank feed will be counted twice if you sync them too. Also turn off any other way payroll was getting into QuickBooks, like QuickBooks Payroll.

    Gusto

    Sync previous payrolls

    2026

    • Sep 25 payrollSync
    • Sep 11 payrollAlready in books
    • Aug 28 payrollAlready in books

  6. Step 6 of 7 · 5 min

    Match bank transactions, don’t add them

    Each synced entry posts to your bank account in QuickBooks. When the matching withdrawals show up in your bank feed (one for net pay, one for taxes), click Match, not Add or Categorize. Adding them records the same payroll a second time. If QuickBooks doesn’t suggest a match, check that the entry date is set to the debit date and the amounts equal the withdrawals.

    Watch out

    If payroll is already doubled: in Banking, open the Categorized tab, click Undo on the duplicate bank transaction, then Match it to Gusto’s journal entry. If that month is already reconciled, ask your accountant before changing it.

    QuickBooks

    Bank transactions

    For review

    • GUSTO NET 5,301.48Match
    • GUSTO TAX 1,609.65Match
    • GUSTO FEE 97.00Categorize

  7. Step 7 of 7 · 5 min

    Check the first entries, then turn on auto-sync

    After your next payroll, open the journal entry in QuickBooks and compare it with Gusto’s payroll summary. Once two or three payrolls check out, turn on auto-sync in Gusto’s Manage tab.

    What a correct entry looks like

    • Gross wages match Gusto’s total gross pay
    • The net pay and tax lines equal the two bank withdrawals exactly
    • Debits equal credits
    • Payroll tax liabilities are back to $0, since Gusto pays the taxes at payroll time

If you use the bank feed instead

Skip the sync and categorize Gusto’s withdrawals as they come into QuickBooks. It’s what I do. Each payroll shows up as separate withdrawals: net pay, taxes, and reimbursements if you have any. Gusto’s monthly fee comes out on its own too.

The catch: the tax withdrawal includes the taxes withheld from employees, not just your employer taxes. Categorizing all of it as payroll tax expense, like I do, keeps things simple and the total cost is right, but wages look lower and payroll taxes higher than your W-2s and quarterly forms show. If your accountant wants those to match, split the tax withdrawal using Gusto’s payroll summary: the employee portion to wages, the employer portion to payroll tax expense.

  • Net pay withdrawal: Wages & Salaries
  • Tax withdrawal: Payroll Tax Expense, or split as above
  • Reimbursements: the expense accounts they belong to
  • Gusto’s monthly fee: Payroll Service Fees
  • Set a QuickBooks bank rule for each so they categorize themselves

Once it’s running

Benefits show as liabilities

Gusto records what you owe a benefit provider. When you pay the provider’s bill, put it against that liability account, not an expense.

Employee taxes sit inside wages

The sync puts employer taxes on their own lines; employee taxes and benefit contributions are included in gross wages.

Reconnecting keeps your mappings

If the connection drops, reconnect from Gusto’s App directory. Gusto says your previous mappings are kept.

Common questions

Why is my Gusto payroll showing up twice in QuickBooks?

Usually because both the synced journal entry and the bank-feed transaction were recorded. Undo the duplicate bank transaction in Banking, then match it to the journal entry.

Do I need the integration to use Gusto with QuickBooks?

No. You can categorize Gusto’s withdrawals from your bank feed instead. You get totals rather than the full wage and tax breakdown.

Can I sync payrolls I ran before connecting?

Yes. Sync this year’s earlier payrolls during setup or later in bulk, but skip any you already recorded and any from periods where you’ve closed the books.

Does Gusto work with QuickBooks Desktop?

Yes. Gusto has a separate integration for QuickBooks Desktop, as well as Xero and FreshBooks.

New to Gusto?

Gusto plus QuickBooks is the setup I run. Sign up through my link and run your first payroll, and Gusto sends you a $100 Visa gift card.

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How to run your first payroll in Gusto →

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