Integrate with QuickBooks Desktop

Step 1: Connect to QuickBooks Desktop from Gusto

You’ll need admin permissions in both Gusto and QuickBooks Desktop to connect your accounts. Start here: 

1. Sign in to your Gusto admin account.
2. Go to the App directory.
3. Search for QuickBooks Desktop and select it.
4. Click Connect.
5. Enter your QuickBooks Desktop credentials.
   • If you're an accounting firm: First, select your firm. Then select the specific company you manage.
6. Click Authorize to allow QuickBooks Desktop and Gusto to sync.
7. Export the chart of accounts from your QuickBooks Desktop account.
   • If you would like to map QuickBooks Desktop Classes to your Journal Entry consolidation options (Employees, Departments, Jobs, or Gusto Projects), be sure to tick the Classes option when exporting your chart of accounts.
8. In Gusto, click Upload IIF file.
   • Select your exported chart of accounts file from the previous step.
9. In the Detailed tab, map your chart of accounts.
   • For more help with mapping, check out the “Map your chart of accounts” section of this article.
   • Important: All Gusto categories must be mapped in order for your sync to work.

Step 2: Automate your mappings (Recommended)

Automating your mappings is optional but recommended to avoid sync errors. This lets you pre-select which QuickBooks Desktop accounts should be used by default for new payroll categories. This means that when a new item is created in Gusto, you will not need to manually map it—Gusto will automatically apply your default mapping.

You’ll manage automated mappings in the Default tab. Click here for 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 any sync preferences—such as whether the sync runs automatically or manually, or whether certain taxes should be consolidated.

Click here for a description of each setting and how to set them up. 

Below is each setting you can customize and how to do so.

Here’s how to get to any of these settings:

1. Sign in to your Gusto admin account.
2. Go to the App directory.
3. Search for QuickBooks Desktop and select it.
4. Under “Settings,” go to the Manage tab.
5. Find the setting you’d like to review. See below to learn more about each setting.

Contractor payment sync

If you pay contractors through Gusto, decide how those payments should sync:

• Batch payments into a single entry (recommended for 30+ contractor payments): All contractor payments for a pay date will sync as one entry. Syncs (including auto-syncs) occur at 5pm PT on the payment processing date.
• Sync each contractor payment as a separate entry: Each contractor payment will appear as its own journal entry.

Employer tax consolidation

Choose how you want employer taxes to appear in QuickBooks Desktop:

• Consolidate: Group all employer taxes into a single lump sum (e.g., "Payroll Taxes").
• Don’t Consolidate: List out individual tax amounts (e.g., Federal Unemployment, Social Security, Medicare, State Unemployment, etc.).

Journal entry consolidation

By default, Gusto consolidates entries of the same type into a single journal entry. You can also choose to group entries:

• By employee
• By department
• By job
• By project (if using Gusto Project Tracking)

To learn more about group mappings, check out the “Group your account mappings and classes” section of this article.

Entry date options

Select when the journal entry should appear in QuickBooks Desktop:

• Check date: This is the date your employees received their payments.
• Debit date: This is the date Gusto initiated the debit for taxes and net pay from your company’s bank account.
• End of pay period: This is the recorded end of the pay period.

Here’s why mapping your chart of accounts matters:

• For payroll data to sync correctly, each payroll item must be mapped to an account in QuickBooks Desktop.
• The more accounts you map to, 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).

Map your chart of accounts

1. In your Gusto admin account, head to the App directory.
2. Choose QuickBooks Desktop.
   • This can be found under the Connected Integrations tab. 
3. Go to the Detailed tab.
4. Click any section (Wages & Salaries, Employer Taxes, etc.) to expand the view.
5. For each Gusto category, click the search box and choose the corresponding QuickBooks Desktop account.
   • By default, Gusto only shows common account types for each category.
   • If you do not see the account you want, start typing the account name to find it.
   • If you've recently added any new charts of accounts in QuickBooks that are not showing up in Gusto, you'll need to manually import a new IIF file.
   • Click here to learn more about types of accounts and commonly used pairings.
6. Repeat until you've selected an account for each Gusto category. Your progress is automatically saved as you go.
   • Unmapped categories will move to the top of the list.

Time-saving tips for the Mapping tab:

• If you’d like 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.

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.

Example: Say you’re setting up default accounts and don’t know what to choose. Gusto might suggest using Payroll Wages for Wages & Salaries, or Payroll Deductions Payable for Deductions.

How suggestions are generated

Gusto’s AI provides recommendations based on:

• Industry standard accounting guidance from US-based 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

Over time, you may make changes to your Gusto account such as adding a custom deduction, creating a new earnings type, or setting up a new benefit. When this happens, new payroll line items are created in Gusto that need to be mapped to an account in QuickBooks Desktop. If these items are not mapped, they can cause sync issues. Setting up default mappings can help you with this.

What default mappings do

Default mappings let you pre-select the QuickBooks Desktop accounts that should be used for new payroll categories. This means that when you create a new line item, you will not have to manually map it to a QuickBooks Desktop account—Gusto will automatically apply your default mapping to it.

• Example: If a new earnings type is created in Gusto, it will appear under "Wages & Salaries." If you’ve already chosen a default mapping for “Wages & Salaries,” the new line item will automatically map to the default QuickBooks Desktop account without interrupting the sync.

Setting up default mappings is optional. If you prefer to manually map new Gusto categories, simply leave the default mapping blank.

Set up default mappings

Follow these steps to set up or change default mappings:

1. In your Gusto admin account, head to the App directory.
2. Go to the Connected Integrations tab.
3. Choose QuickBooks Desktop.
4. Select the Default tab.
5. For each section (Wages & Salaries, Employer Taxes, etc.) you’d like to map, select the QuickBooks Desktop account you want new categories to map to.
   • If you prefer to manually map new categories as they’re created, simply leave the default mapping blank.
6. Repeat for all sections.
   • Your selections are saved automatically.

Edit default mappings

You can change default mappings at any time in the Default tab. Changes will only apply to new mappings going forward. 

Edit detailed mappings

If a new category has been given a default mapping you’d like to change, you can change it in the Detailed tab. Here's how:

1. In your Gusto admin account, go to the App directory. 
2. Go to the Connected Integrations tab.
3. Choose QuickBooks Desktop.
4. Select the Detailed tab.
5. Find the category you’d like to change and select the QuickBooks Desktop account it should map to going forward. 
   • If you also want to change the default mapping for line items in that category going forward, go to the Default tab.

If you want these adjustments to reflect on past payrolls, you'll need to manually re-download the IIF file.

To provide more granularity, you have the option to map your chart of accounts by employee, job, department, or Gusto Projects (available to companies using Gusto Project Tracking). If you use QuickBooks Classes, you can also assign a class to each of the selected grouping options.

This is optional.

Set up consolidated journal entries

Step 1: Choose your journal entry consolidation method

1. Sign in to your Gusto admin account.
2. Go to the App directory and select QuickBooks Desktop.
   • You can also find this under the Connected Integrations tab.
3. Under Settings, go to the Manage tab.
4. Next to "Journal entry consolidation," click Edit.
5. Choose how you want to consolidate entries:
   • By employee: 
     • This can offer more detailed reporting. 
     • Ex: You can track each employee’s wages in separate accounts instead of one "Salaries and Wages" account.
   • By department:
     • This can help you track wages, taxes, and benefits separately. 
     • Ex: 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.
     • Click here to see how you can enable departments.
   • By job:
     • This can split wages, taxes, and benefits by role. 
     • Ex: 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 even more detailed reporting.
     • Click here to see how you can enable multiple job titles for employees.
   • By project:
     • Gusto Project Tracking must be enabled. We do not integrate with QuickBooks Projects.
     • You can track wages, taxes, and benefits by project. 
     • Ex: Instead of all wages going to “Salaries and Wages,” you can split wages into separate accounts for each Gusto Project. 
6. Click Submit.

Step 2: Set up mapping overrides and Quickbooks Classes (optional)

Once you select a consolidation method, a new tab appears on the left. Ex: If you choose to consolidate by employee, the tab will be called Employee. If you choose to consolidate by department, the tab will be called Department.

You can override default mappings for individual employees, departments, jobs, or projects. Overriding a default mapping means assigning different accounts to payroll items at these levels. 

This is optional—if no overrides are applied, journal entries will still be categorized accordingly.

Here's how to set up an override:

1. Find the new tab that corresponds to the consolidation method you chose.
   • Ex: If you chose to consolidate by employee, go to the Employee tab.
2. Click Override.
3. If your company uses QuickBooks Classes, you’ll first have the option to choose a tracking category.
4. Just as you did on the Detailed tab, match each Gusto category to an account in QuickBooks.

Contractor payments

Consolidating journal entries by employee and department is compatible with contractors.

Consolidating by job and project is not compatible with contractors. This is because job titles and Gusto Projects are not currently supported for contractor profiles. If your company pays contractors and uses job or project consolidation, contractor payments will be synced based on the default company mappings.

Unlike online accounting integrations (QuickBooks Online, FreshBooks, and Xero), QuickBooks Desktop does not receive data through an automatic sync because it's an offline product. Data is instead exported to an Intuit Interchange Format (IIF) file, which you will download from Gusto and upload to your QuickBooks Desktop account.

To export your payroll to QuickBooks Desktop, you'll need to first set up QuickBooks Desktop in Gusto—learn how in the Connect to QuickBooks Desktop from Gusto dropdown above. 

1. After you've run payroll, go to the Pay section and select Pay history. 
2. Hover over the payroll you've run and click View details. 
3. Next to "QuickBooks report," click Download. 
   • If you don't see Export, you may need to first connect your QuickBooks Desktop account from your App directory. Learn how in the Connect to QuickBooks Desktop from Gusto dropdown above. 
4. The IIF file will be downloaded onto your computer.
   •  In some cases this will be a ZIP file, a compressed file format. Check out the Windows or Mac instructions to unzip the file.
5. Open QuickBooks Desktop and upload the IIF file.

Troubleshoot upload errors 

Upload errors typically occur when there is a mismatch between the accounts listed in Gusto and the accounts in QuickBooks Desktop. If there are account updates in QuickBooks Desktop, you must upload a new chart of accounts to Gusto. 

Here's how to fix an upload error:

1. Upload a fresh chart of accounts to Gusto.
2. Download a new IIF file for the payroll or contractor payment.
3. If the error persists, review the IIF error file generated by QuickBooks Desktop.
4. After the issues are resolved, upload the payroll’s IIF file to your QuickBooks account again.

Because Gusto does not take any money for benefits or deductions, we include a mapping for a benefit or deduction expense and a benefit or deduction liability. This will create accounts within your accounting software that accrue an amount owed for the benefit or deduction over time.

When the benefit or deduction is then paid to the requesting party, you can offset your liability account and zero out the accrued amount owed.

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 owed 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 owed for the garnishment/deduction.

Important: When money is pulled for an FSA or commuter benefit, before it is deducted through payroll make sure you don't create an expense but rather establish a receivable. It will be expensed in payroll when the amount is deducted. At that point with the deduction, then reduce the receivable.

Offset benefit liabilities

Option 1: Create an entry from the bank debit (created by paying the benefit or deduction) and assign that entry to the liability account to offset.

1. Sign in to your QuickBooks Desktop Account.
2. Go to Banking and select your Bank Feed.
3. Locate the debit from your benefits provider.
4. Click the box to the left-hand side of the debit.
5. Select the liability account from the drop-down menu under "Account."
6. Click Batch Actions - Add.

Option 2: Create a check and associate that check with the liability account to offset.

1. Sign in to your QuickBooks Desktop Account.
2. From Banking, select Write Checks.
3. Manually enter the payment information, and select the liability account from the drop-down menu under Account.
4. Finishing creating the bill.
5. Click Save.

If you pay employees by check, we recommend you print the checks from Gusto.

If you prefer to print checks from within QuickBooks Desktop, you can do this by editing the Journal Entry in QuickBooks Desktop. This prevents double reporting.

For any checks that will be printed 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, you should code the line item to the same liability or clearing account, which will offset the account balance.

Click here for steps to find and edit Journal Entries in QuickBooks Desktop.

Choose a section below for frequently asked questions about this integration.

If you need to troubleshoot the connection or if you no longer want data to sync between Gusto and QuickBooks Desktop, follow the steps below to disconnect the integration. You can reconnect at any time.

1. Sign in to your Gusto admin account.
2. Go to the App directory.
3. Search for and select QuickBooks Desktop.
4. Go to the About tab.
5. Click Disconnect app.