This article is for admins and accountants who want to connect QuickBooks Desktop to Gusto.
QuickBooks Desktop is accounting software that offers industry-specific features and reporting. The software includes inventory tracking, job costing, and online collaboration tools.
Our QuickBooks Desktop integration lets you export your payroll data as an Intuit Interchange Format (IIF) file and upload it into QuickBooks Desktop. The integration works with all QuickBooks Desktop versions that support IIF imports, including Mac, Pro, Premier, and Enterprise.
You can upload your chart of accounts directly from QuickBooks Desktop and use your custom accounts to create a journal entry. You can also add more details to your entries based on the types of earnings and Gusto departments.
Step 1: Set up the connection in Gusto
You need admin permissions in both Gusto and QuickBooks Desktop to connect your accounts.
To set up the connection in Gusto:
Go to the App directory.
Search for QuickBooks Desktop.
Click Learn more.
Click Connect to QuickBooks.
Enter your QuickBooks Desktop credentials.
If you're an accounting firm: First, select your firm. Then select the specific company you manage.
Click Authorize to sync QuickBooks Desktop and Gusto.
Export your chart of accounts from QuickBooks Desktop.
If you want to map QuickBooks Desktop Classes to your journal entry consolidation options (Employees, Departments, Jobs, or Gusto Projects), select the Classes option when you export your chart of accounts.
In Gusto, click Upload IIF file.
Select your exported chart of accounts file from the previous step.
In the Detailed tab, map your chart of accounts.
For more help with mapping, go to the Map your chart of accounts to QuickBooks Desktop section of the article.
Important: You need to map all Gusto categories for your sync to work.
Step 2: Set up automated mapping (recommended)
Automating mapping is optional, but we recommend it to prevent sync errors. This feature lets you choose which QuickBooks Desktop accounts to use by default for new payroll categories. When you add a new item in Gusto, you will not need to map it manually. We'll automatically apply your default mapping.
You'll manage automated mappings in the Default tab. Learn more details and next steps.
Step 3: Choose your sync settings
In the Settings section of the integration, go to the Manage tab to set up your sync preferences, including automatic or manual syncing and the option to consolidate specific taxes.
We let you control how your payroll data syncs to QuickBooks Desktop. You can customize contractor payments, employer taxes, journal entries, and the timing of when entries appear.
To access your sync settings:
Go to the App directory.
Search for QuickBooks Desktop and select it.
Under Settings, go to the Manage tab.
Find the setting you want to review. Learn about each setting below.
Contractor payment sync
If you pay contractors through Gusto, choose how to sync those payments:
Batch payments into a single entry (recommended for 30+ contractor payments): We group all contractor payments for a given pay date into a single entry. We sync payments (including auto-syncs) at 5pm PT on the payment processing date.
Sync each contractor payment as a separate entry: Each contractor payment appears as its own journal entry.
Employer tax consolidation
Choose how employer taxes appear in QuickBooks Desktop:
Consolidate: Group all employer taxes into a single amount (e.g., "Payroll Taxes").
Don't Consolidate: List individual tax amounts (e.g., Federal Unemployment, Social Security, Medicare, State Unemployment).
Journal entry consolidation
By default, we consolidate entries of the same type into a single journal entry. You can also group entries:
By employee
By department
By job
By project (if using Gusto Project Tracking)
To learn more about group mappings, go to the Consolidate QuickBooks Desktop mappings section of the article.
Entry date options
Select when your journal entry appears in QuickBooks Desktop:
Check date: The date your employees received their payments
Debit date: The date we debited taxes and net pay from your company's bank account
End of pay period: The end date of the pay period
Why mapping matters:
You must map each payroll item to a QuickBooks Desktop account for your data to sync correctly.
The more accounts you map, the more detail your journal entries will have.
Having more detailed journal entries gives you more granular reports in QuickBooks Desktop (like Profit & Loss, Expense Reports, and Liability Reports).
How to map your chart of accounts
To map your chart of accounts:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Go to the Detailed tab.
Click any section (Wages & Salaries, Employer Taxes, etc.) to expand the view.
For each Gusto category, click the search box and choose the matching QuickBooks Desktop account.
By default, we only show common account types for each category.
If you cannot find the account you want, start typing the account name.
If you recently added new charts of accounts in QuickBooks that do not appear in Gusto, you need to manually import a new IIF file.
Repeat this process until you've selected an account for each Gusto category. We automatically save your progress as you go.
Unmapped categories move to the top of the list.
Time-saving tips
To map multiple items at once:
Check the box next to each item you want to map.
Click Actions at the top.
Choose Edit account type.
Type the account name and select it.
Click Submit.
To show unmapped items only:
Next to Actions, click the filter icon.
Select Display unmapped accounts only.
Click Apply.
We do not take any money for benefits or deductions. We include a mapping for benefit and deduction liabilities. This creates line items in your journal entry and tracks the amount you owe for the benefit or deduction. When you pay the benefit or deduction to the correct party, you can offset your liability in QuickBooks Desktop and zero out the amount owed.
This integration now includes an AI-powered feature that helps you choose the right accounts when setting up mappings for your chart of accounts. This is especially helpful if you’re not sure which account to pick for a payroll category.
For example, if you’re setting up default accounts and don’t know what to choose, we might suggest using Payroll Wages for Wages & Salaries, or Payroll Deductions Payable for Deductions.
Gusto’s AI gives recommendations based on:
Industry standard accounting guidance from US-based certified public account (CPA) firms.
Common account structures used by thousands of small and mid-sized businesses.
Aggregated, anonymous patterns from other Gusto customers who use platforms like QuickBooks Online, Xero, and FreshBooks.
The AI model never stores or accesses your personal financial information. All suggestions are based on general patterns, not individual data.
Why default mappings matter
When you make changes to your Gusto account (like adding a custom deduction, creating a new earnings type, or setting up a new benefit), we create new payroll line items. You need to map these items to an account in QuickBooks Desktop. If you do not map them, they can cause sync issues. Setting up default mappings can help prevent this problem.
What default mappings do
Default mappings let you choose which QuickBooks Desktop accounts to use for new payroll categories. When you create a new line item, you will not need to map it manually. We'll automatically apply your default mapping.
Example: You create a new earnings type in Gusto. It appears under "Wages & Salaries." If you already set a default mapping for "Wages & Salaries," the new line item automatically maps to your default QuickBooks Desktop account. Your sync continues without interruption.
Setting up default mappings is optional. If you prefer to map new Gusto categories manually, leave the default mapping blank.
Set up default mappings
To set up default mappings:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Select the Default tab.
For each section (e.g., Wages & Salaries, Employer Taxes) you want to map, select the QuickBooks Desktop account where new categories should map.
If you prefer to map new categories manually when you create them, leave the default mapping blank.
Repeat for all sections.
We automatically save your selections.
Edit default mappings
You can change default mappings at any time in the Default tab. Your changes only apply to new mappings going forward.
Edit detailed mappings
If a new category uses a default mapping you want to change, you can change it in the Detailed tab.
To edit detailed mappings:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Select the Detailed tab.
Find the category you want to change and select the QuickBooks Desktop account it should map to going forward.
If you also want to change the default mapping for future line items in that category, go to the Default tab.
If you want these changes to appear on past payrolls, you need to manually re-download the IIF file.
You can add more detail to your chart of accounts by mapping it by employee, job, department, or Gusto Projects (available to companies that use Gusto Project Tracking). If you use QuickBooks Classes, you can also assign a class to each grouping option.
This step is optional.
Step 1: Choose how to consolidate your journal entries
To choose how to consolidate your journal entries:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Under Settings, go to the Manage tab.
Next to Journal entry consolidation, click Edit.
Choose how you want to consolidate entries:
By employee:
This gives you more detailed reporting.
Example: You can track each employee's wages in separate accounts instead of one "Salaries and Wages" account.
By department:
This helps you track wages, taxes, and benefits separately.
Example: You can send Design wages to one account and Marketing wages to another, instead of combining everything into "Salaries and Wages." You can also map departments to QuickBooks Classes if needed.
By job:
This can split wages, taxes, and benefits by role.
Example: You can track cashier wages and cook wages in separate accounts instead of sending all wages to "Salaries and Wages." If you use QuickBooks Classes, you can also map jobs to Classes for more detailed reporting.
By project:
You must first turn on Gusto Project Tracking. We do not integrate with QuickBooks Projects.
You can track wages, taxes, and benefits by project.
Example: Instead of sending all wages to "Salaries and Wages," you can split wages into separate accounts for each Gusto Project.
Click Submit.
Step 2: Set up mapping overrides and QuickBooks Classes (optional)
When you select a consolidation method, a new tab appears on the left. For example, if you choose to consolidate by employee, the tab will be labeled Employee. If you consolidate by department, the tab will be labeled Department.
You can override default mappings for individual employees, departments, jobs, or projects. When you override a default mapping, you assign different accounts to payroll items at these levels.
This step is optional. If you do not apply overrides, we still categorize your journal entries correctly.
To set up an override:
Find the new tab that matches the consolidation method you chose.
Example: If you consolidated by employee, go to the Employee tab.
Click Override.
If your company uses QuickBooks Classes, you can first choose a tracking category.
Match each Gusto category to an account in QuickBooks, just like you did on the Detailed tab.
How consolidating works with contractor payments
You can consolidate journal entries by employee and department when you pay contractors.
You cannot consolidate by job or project when you pay contractors. Job titles and Gusto Projects are not currently supported for contractor profiles. If your company pays contractors and uses job or project consolidation, we sync contractor payments using your default company mappings.
Because it's an offline product, QuickBooks Desktop does not sync data automatically like online accounting integrations (QuickBooks Online, FreshBooks, and Xero). Instead, you export data to an Intuit Interchange Format (IIF) file. You download this file from Gusto and upload it to your QuickBooks Desktop account.
Before exporting payroll to QuickBooks Desktop, you need to set up QuickBooks Desktop in Gusto. Learn how in the Connect QuickBooks Desktop to Gusto section of the article.
To export payroll:
After you run payroll, go to Pay.
Select Pay history.
Hover over the payroll you ran and click View details.
Next to QuickBooks report, click Download.
If you do not see Export, you may need to connect your QuickBooks Desktop account from your App directory first. Learn how in the Connect QuickBooks Desktop to Gusto section of the article.
The IIF file will download to your computer.
Open QuickBooks Desktop and upload the IIF file.
Fix QuickBooks Desktop upload errors
Upload errors usually happen when the accounts in Gusto do not match the accounts in QuickBooks Desktop. If you update accounts in QuickBooks Desktop, you must upload a new chart of accounts to Gusto.
To fix an upload error:
Download a new IIF file for the payroll or contractor payment.
If the error continues, review the IIF error file from QuickBooks Desktop.
After you fix the issues, upload the payroll's IIF file to your QuickBooks account again.
We do not take money for benefits or deductions. We include a mapping for both benefit and deduction expenses, as well as benefit and deduction liabilities. This creates accounts in your accounting software that track the amount you owe for the benefit or deduction over time.
When you pay the benefit or deduction to the requesting party, you can offset your liability account and zero out the amount you owe.
Benefits always have two line items on the journal entry:
Employer Benefit Expense: This tracks the cost of employer contributions to benefits.
Benefit Liabilities: This tracks the amount you owe to the benefit provider. It's the total of employee deductions + employer contributions.
Garnishments always have one line item on the journal entry for the garnishment liability. It tracks the amount you owe for the garnishment or deduction.
Important: When we withdraw from a flexible spending account (FSA) or commuter benefit before the amount is deducted from payroll, make sure you do not create an expense. Instead, set up a receivable. We'll expense the amount in payroll when we deduct it. At that point, reduce the receivable with the deduction.
Option 1: Create an entry from the bank debit (created by paying the benefit or deduction) and assign it to the liability account.
To do this:
Sign in to your QuickBooks Desktop account.
Go to Banking and select your Bank Feed.
Find the debit from your benefits provider.
Click the box to the left of the debit.
Select the liability account from the drop-down menu under Account.
Click Batch Actions - Add.
Option 2: Create a check and link it to the liability account.
To do this:
Sign in to your QuickBooks Desktop account.
From Banking, select Write Checks.
Manually enter the payment information, and select the liability account from the drop-down menu under Account.
Finish creating the bill.
Click Save.
If you pay employees by check, we recommend printing the checks through Gusto.
If you prefer to print checks from QuickBooks Desktop, you need to edit the journal entry in QuickBooks Desktop. This prevents double reporting.
For any checks you print from QuickBooks Desktop, we recommend updating the bank account line item on the journal to a liability account or clearing account. When you create the check in QuickBooks Desktop, code the line item to the same liability or clearing account. This offsets the account balance.
Learn how to find and edit journal entries in QuickBooks Desktop.
Expand the sections for frequently asked questions about the QuickBooks Desktop integration.
Q: Do you support QuickBooks Classes?
A: Yes. Go to the Consolidate QuickBooks Desktop mappings section of the article.
Note: If you want to map QuickBooks Desktop Classes to your journal entry consolidation options (employees, departments, jobs, or Gusto Projects), select the Classes option when exporting your chart of accounts.
Q: My chart of accounts in Gusto does not look correct. What should I do?
A: Unlike online accounting integrations like QuickBooks Online, QuickBooks Desktop is an offline product and does not sync data automatically.
If your chart of accounts appears incorrect, upload a fresh chart of accounts. For steps to upload a new IIF file, go to the Connect QuickBooks Desktop to Gusto section of the article.
Note: We do not currently support Accounts Receivable and Accounts Payable account types because these require a Contact with the Account. We support Asset and Liability accounts without a Contact.
Q: How do I handle checks?
A: We recommend printing checks from your Gusto account or handwriting them. You can then reconcile the journal entry from Gusto when your employees cash the checks. We include the amount of each check in the journal entry.
Q: Why can't I find the QuickBooks account I need in the drop-down menu?
A: The initial list in the drop-down menu shows recommended accounts based on the category you selected. To choose a different account, type the account name into the search box.
If you still cannot find the account, upload a new chart of accounts. Go to the Connect QuickBooks Desktop to Gusto section of the article.
Q: Do I need to select a default for each section?
A: No, you do not need to select a default for every section. If you prefer to map specific sections manually, leave those sections blank.
Q: What happens if I do not set up default mappings?
A: Default mappings automatically map new payroll categories that you add to your integration. If you do not turn on default mappings, you need to manually select the correct account for each new payroll category.
You cannot download journal entries until you map all categories to an account in QuickBooks Desktop. This may disrupt your integration process.
Q: When does Gusto create new mapping categories?
A: We may create new categories in your integration when you:
Add a deduction.
Create a new earning type.
Set up a benefit for the first time.
Set up a new time-off policy.
Move to new states.
Request payroll adjustments.
Each of these actions can introduce new payroll categories that you need to map to keep your integration running smoothly.
Q: If I set up or change default mappings, will that change what I already mapped on the Detailed tab?
A: No. This only affects new categories that you add to your integration in the future. To adjust your detailed mappings, you can do so manually from the Detailed tab.
Q: Can I change my default mapping later?
A: Yes, you can change your default mappings at any time.
Note: Any changes will only affect future mappings. Your existing mappings stay the same.
Q: If I update my mappings, can I re-sync a payroll to update the bill or journal entry?
A: Yes. To re-sync a payroll:
After you update your mappings, go to Pay.
Choose Pay History.
Download a new IIF file.
Q: How do I break out individual employee payroll items?
A: You can change the journal consolidation method to "by employee."
To do this:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Under Settings, go to the Manage tab.
Next to Journal entry consolidation, click Edit.
Select Employee.
Q: Why can't I find the QuickBooks account I need in the drop-down menu?
A: The initial list in the drop-down menu shows recommended accounts based on the category you selected. To choose a different account, type the account name into the search box.
If you still cannot find the account, upload a new chart of accounts. Go to the Connect QuickBooks Desktop to Gusto section of the article for steps to upload a new IIF file.
Q: What if I will not be using one of the payroll items listed?
A: You still need to map the item to an account. If the payroll item does not apply to you, no data will be synced related to the account selected in your entry. Only payroll items that apply to a processed payroll will appear in the synced entry.
Q: Can I include employee benefit deductions on the journal entry?
A: We include employee deductions in the gross wages amounts that appear on the journal entry. We do not track these separately because they're not an extra expense to the company beyond what we already report for wages.
We include employee deduction amounts in the Benefit Liability along with the Employer Contributions. Go to the Offset benefit liabilities in QuickBooks Desktop section of the article for more information.
Q: Can I break out unique reimbursements through separate mappings?
A: No, we push all reimbursements over as a lump sum (e.g., Cell Phone Reimbursement + Gym Reimbursement + Office Supplies Reimbursement).
Q: Can I use more than one tracking category or journal consolidation method? For example, can I consolidate my journal entries by employee and by job?
A: No, not at this time. You need to choose a single consolidation method (by employee, department, job, or project). Next, you may select one class for each employee, department, job, or project.
Q: Can I change how I consolidate my mappings?
A: Yes, you can change your consolidation preferences at any time. Under Settings, go to the Manage tab.
Important: We'll delete any previous consolidated account mapping overrides when you make changes. We'll keep your company's Detailed mappings.
Q: Do I need to set up overrides for consolidated mappings?
A: No. Setting up overrides for consolidated mappings is optional. While you do not need to do this, it lets you customize the mapping layout for each unique grouping you set up.
Q: Do I need to set up a QuickBooks Class for each consolidated grouping?
A: No, this is optional based on your specific needs.
Q: Can I assign multiple QuickBooks Classes to a single consolidated grouping?
A: No, you can only assign one QuickBooks class per consolidated grouping right now.
Q: Does Gusto integrate with QuickBooks Projects?
A: No, we do not currently integrate with QuickBooks Projects. If you choose to consolidate your mappings by project, we'll split each entry according to the projects you set up in your Gusto Project Tracker. However, we will not push this information directly to QuickBooks Projects.
Q: Why do I get an error when I try to upload journal entries to QuickBooks Desktop?
A: Upload errors usually happen when the accounts in Gusto do not match the accounts in QuickBooks Desktop.
To fix an upload error:
Upload a fresh chart of accounts to Gusto.
Download a new IIF file for the payroll or contractor payment.
If the error persists, review the IIF error file from QuickBooks Desktop.
After you fix the issues, upload the payroll's IIF file to your QuickBooks account again.
Q: If I update my mappings, can I re-sync a payroll to update the bill or journal entry?
A: Yes. To re-sync a payroll:
After updating your mappings, go to Pay.
Choose Pay History.
Download a new IIF file.
Q: How do employee taxes and employee benefit contributions sync to QuickBooks Desktop?
A: We always include them in Gross Wages & Salaries.
Q: Do you break out individual taxes?
A: We handle all of your tax payments automatically. Because of this, you do not need to track tax liabilities. When we sync entries, we record employer taxes as expenses.
You can choose to break out employer taxes by each tax or lump them together. You'll find this option under Settings in the Manage tab.
At this time, we only support one account mapping, which will be used for all employer taxes.
We do not break out employee taxes individually for mapping or in journal entries, as these values are included in Gross Wages.
Q: How do contractor payments sync over?
A: You have two options for syncing contractor payments. Go to the Customize QuickBooks Desktop sync settings section of the article for more information.
Q: Can I sync non-US contractor payments to QuickBooks Desktop?
A: Yes, you can sync both US-based and non-US-based contractor payments. To do so, go to the Pay section in Gusto and choose Pay history. Go to the Contractor payment history tab and select a payment to sync.
Q: Can I sync non-US employee payrolls to QuickBooks Desktop?
A: No, not at this time.
Q: Can I sync Gusto or NEXT insurance invoices to QuickBooks Desktop?
A: No, not at this time.
If you need to troubleshoot the connection or if you no longer want Gusto and QuickBooks Desktop to sync data, disconnect the integration. You can reconnect at any time.
To disconnect QuickBooks Desktop from Gusto:
Go to the App directory.
Go to the Connected Apps tab.
Choose QuickBooks Desktop.
Click Manage.
Under the Settings tab, click Manage.
On the right, click Disconnect app.
Going forward, data will no longer sync between Gusto and QuickBooks Desktop.