Availability: This integration is currently in beta and is not available to all users. To access, sign up for the QBO Beta.
This article explains how to connect Patriot Payroll to QuickBooks Online (QBO) and configure your mapping settings so that payroll journal entries are automatically sent to your QBO account each time you run payroll in Patriot.
If you use QuickBooks Desktop instead, see Exporting Patriot Payroll into QuickBooks Desktop via IIF.
If you use Patriot Accounting, see Integrating Patriot Payroll with Patriot Accounting.
Video Walkthrough
Video summary: This video walks through connecting your Patriot Payroll account to QuickBooks Online and completing your initial mapping setup. It covers navigating to Payroll Integration Options, authorizing the QBO connection, selecting your journal entry type, setting up clearing accounts, and mapping wages, taxes, deductions, and contributions to QBO accounts.
To connect Patriot Payroll to QuickBooks Online:
Go to Settings > Payroll Settings > Payroll Integration Options.
Select QuickBooks Online and click Connect to QuickBooks.
The QuickBooks Online sign-in page will open. Enter your QuickBooks Online email or user ID and password.
If you have multiple QuickBooks Online accounts under the same login, select the account you want to connect.
A confirmation popup will appear once your QuickBooks Online account is successfully connected.
Choose Integration Options
After connecting, answer the following setup questions to control how Patriot sends payroll data to QuickBooks Online.
1. Journal Entry Type
Select how payroll journal entries will be imported into your QuickBooks Online account:
Summary: All employee payroll is combined into a single total sent to each QBO account you select.
Line-by-line employee detail: Journal entries are broken out by individual employee.
2. Do You Use Clearing Accounts?
A clearing account is a temporary liability account in your QuickBooks Online general ledger — not a dedicated payroll bank account. It holds payroll liabilities (such as taxes and deductions withheld from employee pay) until those amounts clear your bank. As you reconcile each item, you move it from the clearing account to the appropriate specific account in your general ledger. A clearing account should have a zero balance once all items are fully posted.
Select Yes if you use a clearing account in QBO for payroll liabilities. Select No if you do not.
3. Which QBO Account Will Taxes Be Collected From?
Choose the asset account — typically a bank account — that Patriot will withdraw tax payments (and direct deposit funds, if applicable) from.
4. Map All Employees to the Same Accounts?
Select Yes if all employee payroll journal entries post to the same expense and liability accounts.
Select No if different employees need to post to different accounts (for example, if owner payroll goes to a separate account). When you select No, you will create separate mapping profiles. See Create Mapping Profiles for Journal Entries below.
Map Wages, Taxes, and Expenses to QBO Accounts
This section controls which QuickBooks Online accounts receive your payroll expenses and liabilities. The options available for some fields depend on whether you have Basic Payroll or Full Service Payroll, and whether you use clearing accounts.
Gross Pay
Select the QBO expense account you want gross pay applied to.
Hour or Money Types
To map specific money types or hour types to separate QBO expense accounts, click +Map Hour and Money Types to Account. For example, you can map Bonus, Commission, and Expense Reimbursement each to a different expense account.
Employee Tax
The Employee Tax field options depend on your Patriot plan and clearing account selection:
Basic Payroll: Employee Tax maps to a liability account.
Full Service Payroll, no clearing account, tax filing setup complete: This field does not appear. Employee taxes default to the bank account selected in the "Which QBO account will your taxes be collected from?" question above.
Full Service Payroll with clearing account: Select the QBO clearing account you use for employee taxes.
To map specific employee taxes to individual QBO accounts, click +Map Employee Tax to Account, select the tax type and corresponding QBO account, then click +Add Row to add more mappings.
Employer Tax (Expense)
Select the QBO expense account that employer tax expenses should be applied to. Click +Add Row to map additional employer taxes to specific expense accounts.
Employer Tax (Remittance)
The Employer Tax (Remittance) field options depend on your Patriot plan and clearing account selection:
Basic Payroll: Employer Tax (Remittance) maps to a liability account.
Full Service Payroll, no clearing account, tax filing setup complete: This field does not appear. Employer taxes default to the bank account selected in the "Which QBO account will your taxes be collected from?" question above.
Full Service Payroll with clearing account: Select the QBO clearing account you use for employer taxes.
To map specific employer taxes, click +Map Employer Tax to Account, select the tax type and corresponding QBO account.
Direct Deposit
This field only appears if direct deposit is active in your Patriot account. Options depend on your plan and clearing account selection:
Basic Payroll, no clearing account: Select the asset account (typically a bank account) that direct deposit funds will be withdrawn from.
Full Service Payroll with clearing account and active direct deposit: Select the QBO clearing account to apply direct deposit to.
Full Service Payroll, no clearing account, active direct deposit: This field does not appear. Direct deposit will be withdrawn from the bank account selected in the "Which QBO account will your taxes be collected from?" question above.
Net Pay
Select the bank account you want payroll checks withdrawn from. If you use both direct deposit and paper checks, the Net Pay field reflects only the paper check amounts — not direct deposit amounts.
Map Employee Deductions to QBO Accounts
Deduction mapping is required even if no deductions are currently set up in your Patriot account.
Choose the default QBO liability account to assign to employee deductions.
To map specific deductions to individual liability accounts, click +Map Employee Deduction to Account.
Click +Add Row to add more deduction-to-account mappings.
Map Company-Paid Contributions
Contribution mapping is required even if no contributions are currently set up in your Patriot account.
Choose the default QBO liability account to assign to company-paid contributions.
To map specific contributions to individual liability accounts, click +Map Company-Paid Contribution to Account.
Click +Add Row to add more contribution-to-account mappings.
Create Mapping Profiles for Journal Entries
Mapping profiles let you assign different QBO accounts to different groups of employees. For example, you can send owner payroll to a separate account from regular employee payroll. You can assign multiple employees to the same profile, or create as many profiles as your accounting needs require.
To use mapping profiles, you must select No when asked "Do you want to map all employee payroll to the same expense and liability accounts?" during the Choose Integration Options step. If you selected Yes, profiles are not available.
From Payroll Integration Options, confirm No is selected for the question "Do you want to map all employee payroll to the same expense and liability accounts?" Once No is selected, you will see the option to create and name multiple profiles.
Enter a Mapping Profile Description — a descriptive name for this profile. The profile name will appear in the description field of your QBO journal entries.
Select the employees to assign to this profile. Only active employees not already assigned to another profile will appear in the list.
Map the wage, tax, and expense accounts for this profile. You can map to broad default accounts or get as specific as needed for each account type.
When finished mapping, choose a save option:
Save: Saves the profile as-is.
Save and Duplicate: Creates an exact copy of the profile, including the name. Rename the duplicate to distinguish the two.
Save and Create New: Opens a blank new profile with no settings carried over from the previous profile.
Note: If you selected Summary as your journal entry type, each mapping profile will generate a separate summary journal entry in QBO.
Disconnect Your QBO Account
If you no longer want Patriot Payroll to integrate with QuickBooks Online, you can disconnect your QBO account from within Patriot. Disconnecting removes all QuickBooks Online account information from Patriot Software.
After disconnecting:
Previous payroll transaction history remains viewable in the QuickBooks Integration Status Report in Patriot.
If you later connect Patriot Payroll to Patriot Accounting, your QuickBooks Online connection will be automatically disconnected at that time.
Frequently Asked Questions
Can I post past payrolls once I set up the QuickBooks Online integration?
Past payrolls cannot be posted through the QuickBooks Online integration. Only new payrolls run after the QBO connection is established will be sent to QuickBooks Online.
Can I delete a mapping profile?
Mapping profiles cannot be deleted after they are created. You can remove all employees from a profile so Patriot will not include that profile when sending journal entries to QuickBooks Online.
I don't see all of my employees in the dropdown when creating a profile. Why?
An employee missing from the profile dropdown is likely already assigned to a different mapping profile. Each active employee can only be assigned to one profile at a time, so Patriot will not show that employee as an option in additional profiles.
Does the QBO integration send over contractor payroll?
The QBO integration does not send contractor payroll. Only W-2 employee payroll is included. Contractor (1099) payroll is not sent to QuickBooks Online.
Do I have to assign all employees to a mapping profile?
If you selected that all employee payroll maps to the same accounts, you do not need to create mapping profiles at all. However, once you create a profile and assign at least one employee to it, all employees in your Patriot account must be assigned to a profile.
How do I add another mapping profile after saving my first one?
After saving your first profile, click Save and add another or Save and duplicate. If you saved without creating additional profiles, go to an existing profile, click Edit, scroll to the bottom, and select either Save and create new or Save and duplicate.