This article is for admins who want to integrate Gusto with FreshBooks.
FreshBooks offers cloud-based accounting software for service-based small businesses. FreshBooks includes time tracking, expense tracking, and invoicing.
Our integration with FreshBooks syncs detailed payroll expenses into your FreshBooks account. We sync your payroll expenses automatically. You can organize expenses within FreshBooks by expense type and Gusto department.
Option 1: Connect to FreshBooks from Gusto
You need admin permissions in both Gusto and FreshBooks to connect your accounts.
To set up the connection in Gusto:
Go to the App directory.
Search for FreshBooks.
Click Learn more.
Click Connect.
Enter your FreshBooks credentials.
If you’re an accounting firm: First, select your firm. Then select the specific company you manage.
Click Authorize to sync FreshBooks and Gusto.
In the Detailed tab, map your chart of accounts.
For more help with mapping, go to the Map your FreshBooks chart of accounts section of the article.
Important: You need to map all Gusto categories for your sync to work.
Option 2: Start a new Gusto account from FreshBooks
To sign up for Gusto from FreshBooks with 2 months of free payroll:
In the top-left corner, click the gear icon.
Click Payroll Settings.
Click Create a Trial Account for a free 2-month trial.
Gusto will open so you can set up your company account.
After you set up your Gusto account, go to the App directory on the left.
In the Find an app search bar, type “FreshBooks.”
Choose FreshBooks.
Click Connect.
Enter your FreshBooks login credentials.
Click Allow Access to authorize Gusto to access your FreshBooks account.
Choose the business(es) you want Gusto to connect to.
Click Connect to FreshBooks.
Automating mapping is optional, but we recommend it to prevent sync errors. This feature lets you choose which FreshBooks 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. Click here for more details and next steps.
In the Settings section of the integration, stay on the Manage tab to set up your sync preferences, including automatic or manual syncing and the option to consolidate specific taxes.
Go to the Customize FreshBooks sync settings section of the article for a description of each setting and how to set them up.
You can customize how we sync payroll data to FreshBooks. This section explains each setting and shows you how to access them.
To access your sync settings:
Go to the App directory.
Search for FreshBooks and select it.
Under Settings, go to the Manage tab.
Find the setting you want to review. See below for more information about each setting.
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 will appear as its own journal entry.
Employer tax consolidation
Choose how you want employer taxes to appear in FreshBooks:
Consolidate: Group all employer taxes into a single amount (e.g., “Payroll Taxes”).
Don’t Consolidate: List out 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 FreshBooks mappings section of the article.
Entry date options
Select when your journal entry appears in FreshBooks:
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 FreshBooks account for your data to sync correctly.
The more accounts you map, the more detail your invoice will have.
Having more detailed invoices gives you more granular reports in FreshBooks.
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 FreshBooks.
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 FreshBooks 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 still cannot find an account you’d like to use, create the account in FreshBooks, then click Refresh chart of accounts in Gusto.
Click here to learn more about account types and common pairings.
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.
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 FreshBooks. 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 FreshBooks 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 FreshBooks account. Your sync continues without interruption.
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
To set up default mappings:
Go to the App directory.
Go to the Connected Apps tab.
Choose FreshBooks.
Select the Default tab.
For each section (e.g., Wages & Salaries, Employer Taxes) you’d like to map, select the FreshBooks 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 progress.
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 FreshBooks.
Select the Detailed tab.
Find the category you want to change and select the FreshBooks 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 synced past payrolls to FreshBooks with incorrect mapping, you need to manually re-sync them.
You can add more detail to your chart of accounts by mapping it by employee, job, department, or Gusto Projects (available to companies using Gusto Project Tracking).
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 FreshBooks.
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 can help 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.”
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.”
Click here to learn how to turn on multiple job titles for employees.
By project:
You must first turn on Gusto Project Tracking.
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
When you select a consolidation method, a new tab appears on the left. 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 detailed mappings for individual employees, departments, jobs, or projects. When you override detailed mappings in this tab, you assign different accounts to payroll items at these levels. This will not impact your mappings in the Detailed tab.
This step is optional. If you do not apply overrides, we still categorize journal entries based on what is set on the Detailed tab.
To override your mappings by consolidated category:
Find the new tab that matches the consolidation method you chose.
Example: If you consolidated by employee, go to the Employee tab.
Click Edit.
If you want to adjust your mappings for this specific consolidation, select the new chart of accounts from the dropdown for the matching Gusto category.
This only applies to this specific consolidation.
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.
You can manually sync payroll data to FreshBooks at any time. If you turn on autosync, we sync the data automatically when you process payroll.
To manually sync your payroll data to FreshBooks:
Go to Pay.
Select Pay history.
Click the payroll or contractor payment you want to sync.
At the top of the Payroll detail page, click Sync.
Note: If you turned on autosync, we automatically push data when you process payroll.
A timestamp will appear to confirm we pushed the data to FreshBooks.
Sign in to your FreshBooks account.
After syncing, individual payroll expenses appear in “Expenses” in FreshBooks as 3 expense entries: total wages, total taxes, and total reimbursements. Contractor payments appear separately with the contractor’s name, and you do not need to approve the expense.
You can reconcile and match expenses with bank withdrawals in two ways when you use accounting software.
Go to the bank transactions from your bank account integration. When you find a withdrawal, create a matching expense.
Example: You bought items at the office supply store. You find this bank withdrawal in your bank transactions. You can now add a matching office supply expense. This accounts for the expense and shows the cash reduction.
Report a future expense. When you find the actual cash transaction, match it to the expense you reported earlier.
Example: You forecast that supplies will cost $X at the beginning of the month, but you pay at the end of the month. So you report the expense. When you pay at the end of the month, you can match the expense you reported to this bank transaction.
When you print paper checks using your accounting software, you might find an extra expense on your books. This happens because we report total gross wages, whether you pay your employees by direct deposit or by check.
This can cause issues when you reconcile your expenses. The amount you pay to employees may be over-reported.
We recommend printing checks from your Gusto account or handwriting them. This prevents expenses from appearing as over-reported. Then you can easily reconcile the total payroll expense from Gusto when your employees cash their checks.
If you do not handwrite or print your checks through Gusto, here are the best options to avoid over-reporting.
Example of over-reported checks
You run a payroll that costs $10,000. Your employee gets a $7,000 check from you. In the $10,000 expense that Gusto synced, you can find line items for $9,000 of gross wages. This includes a $7,000 check and $2,000 in employee taxes. The expense also includes $1,000 of employer payroll taxes.
When you create a check for your employee in your accounting software, it also creates an expense for $7,000. As a result, when you look at your total payroll expenses, payroll for this period shows $17,000. When reconciling your books, however, only $10,000 leaves your checking account: $3,000 for employee and employer taxes, and $7,000 from the cashed check.
The check your accounting software created led you to over-report your payroll expenses. When you look at your profit for the year, it looks lower than it should be. You need to use one of the solutions in this section to reconcile the over-reported check payment.
Steps to reconcile checks
Reduce the expense account linked to Gross Wages by the amount of the employee’s check before you create the check in your FreshBooks account. Your mappings in Gusto show the expense account. When you reduce the Gross Wage expense by the check amount, you prevent double-counting.
Example: You sync a total payroll expense of $10,000. You know that when you create a check, you’ll over-report the expense by $7,000. So you reduce the Gross Wage expense from $9,000 to $2,000.
Edit a Gusto FreshBooks expense
To edit a Gusto FreshBooks expense:
Go to Expenses.
Select the expense item for Regular Wages.
Click Edit.
Reduce the entry by the amount of the check.
FreshBooks does not support liabilities. Handle your benefit expenses directly in FreshBooks.
Expand the sections for frequently asked questions about the FreshBooks integration.
Q: My chart of accounts in Gusto does not look correct. What should I do?
A: First, click Refresh chart of accounts in Gusto. If this does not fix the issue, you may have linked the wrong FreshBooks account. Disconnect the integration and reconnect to the correct FreshBooks account.
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 FreshBooks account I need in the drop-down?
A: The initial list in the drop-down menu shows recommended accounts based on the category you selected. To choose a different account, simply type the account name into the search box.
If you still cannot find the account, you might need to create it in FreshBooks first. Once you create the account, click Refresh chart of accounts and search for it again in the search box.
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.
Note: The sync pauses until you map all categories to an account in FreshBooks. This may disrupt your integration.
Q: When does Gusto create new mapping categories?
A: We may create new categories in your integration when you:
Create a new earning type
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. Changes to default mappings only apply to new categories added in the future. If you have unmapped categories in that section, you can apply the default account to those categories to map them quickly. You can still manually update any existing detailed mappings on the Detailed tab.
Q: Can I change my default mapping selections later?
A: Yes, you can change your default mapping selections at any time. Your changes only affect future mappings. Your existing mappings stay the same unless you resync the entry.
Q: If I update my mappings, can I re-sync a payroll to update the entry?
A: Yes. In FreshBooks, make sure to delete the original entries that Gusto synced before or after you re-sync the payroll.
To re-sync a payroll:
Go to Pay.
Choose Pay History.
Select the check date.
At the top of the page, click Re-sync.
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.
Select FreshBooks.
Go to Settings.
Choose Manage.
Next to Journal entry consolidation, click Edit.
Select Employee.
Q: Why can’t I find the FreshBooks account I need in the drop-down?
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, you might need to create it in FreshBooks first. Once you’ve created the account, click Refresh chart of accounts in Gusto and search for it again in the search box.
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 within the synced entry.
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 bills or journal entries by employee and by job?
A: No, not at this time. You must 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. Note that we’ll delete any previous consolidated account mapping overrides when you make changes.
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: Why didn’t my sync work?
A: A sync might stop working if you disconnect your FreshBooks integration or if account mappings are missing.
Reconnect FreshBooks: If your integration disconnected, follow the steps in the Connect your FreshBooks account to Gusto section of the article to reconnect.
Check for missing mappings: To make sure you mapped all payroll categories, go to the Detailed tab and review each section. If an account is not mapped, a red pill shows in that section. To fix this, refer to the Map your FreshBooks chart of accounts section of the article.
Q: Why did Gusto disconnect from FreshBooks?
A: The integration might disconnect because of an authorization issue.
To reconnect the integration:
Go to the App directory.
Search for FreshBooks.
Click Connect.
Enter your admin credentials.
After you reconnect, all your previous mappings should remain.
Q: If I update my mappings, can I re-sync a payroll to update the journal entry?
A: Yes. Each sync creates a new expense in FreshBooks. Make sure to delete the original entries that Gusto synced before or after you re-sync the payroll.
To re-sync a payroll:
Go to Pay.
Choose Pay History.
Select the check date.
At the top, click Re-sync.
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. Click here to learn more.
Q: Is there a way to retroactively sync all payrolls once I turn on auto-sync?
A: Auto-sync only works for payrolls after you turn it on. You need to manually sync any payrolls you ran before you turned on auto-sync.
Q: What does the timestamp show?
A: The exact time we synced a payroll to FreshBooks
Q: Can I re-sync an entry that has already been reconciled?
A: Yes. Each sync creates a new expense in FreshBooks. Delete the expense in FreshBooks. Then, re-sync the payroll.
Q: Can I sync international employee payrolls to FreshBooks?
A: No, not at this time.
Q: Can I sync Gusto or NEXT insurance invoices to FreshBooks?
A: No, not at this time.
Check out FreshBooks’ help center.