By Amanda Pierce, payroll systems support lead with 10 years of experience helping small businesses onboard employees and correct payroll setup errors
Last reviewed: July 22, 2026
FreshBooks business owners use their normal FreshBooks login to set up and run FreshBooks Payroll powered by Gusto. Employees and contractors should be added through their own team profiles rather than receiving the owner’s account credentials.
This independent guide is not affiliated with FreshBooks.
The first job is confirming whether the problem concerns account login, payroll approval, employee onboarding, the payroll deadline, or missing tax information. These stages use different screens and cannot be fixed with one general password reset.
What FreshBooks Payroll Is
FreshBooks Payroll is a U.S. payroll service powered by Gusto and built into eligible FreshBooks business accounts. Owners can onboard employees and contractors, run payroll, review payment history, access reports, and manage payroll tax documents from FreshBooks.
FreshBooks also describes a separate Gusto option for businesses with larger teams or more complex payroll and human-resources needs. That version is accessed through a separate Gusto account rather than entirely through the integrated FreshBooks Payroll experience.
The distinction matters.
A business using integrated FreshBooks Payroll should begin in FreshBooks. A company using a separate Gusto account may need to sign in to Gusto for payroll administration, even though payroll entries can be connected to FreshBooks accounting.
Choose the Correct FreshBooks Route
| Your task | Correct starting point |
|---|---|
| Manage FreshBooks Payroll | FreshBooks business login |
| Recover account access | Forgot Your Password? |
| Add an employee or contractor | Team Members profile |
| Complete payroll setup | Payroll onboarding |
| Run regular or off-cycle payroll | Payroll run controls |
| Review prior payroll runs | Payment History |
| View payroll reports or forms | Payroll > More Actions |
| Correct a team sync warning | Team member’s Payroll sections |
| Investigate a broad outage | FreshBooks status page |
The FreshBooks login page currently provides email and password fields, Google and Apple sign-in, Forgot Your Password?, Can’t Log In?, and language controls.
Do this first: confirm the active business after login. Skip payroll changes when the company name does not match the employer you intend to pay.
Log In Before Troubleshooting Payroll
FreshBooks supports direct credentials as well as Google and Apple authentication. FreshBooks recommends disabling browser autofill and typing login information manually when saved details appear correct but continue to fail.
Users who normally select Sign in with Google or Sign in with Apple should recover that provider’s password through the provider. A separate FreshBooks password can be added through Account Profile before disconnecting Google or Apple access.
Do not create a second business account because Payroll appears missing. Another account will not contain the established employees, pay schedule, tax setup, historical payroll runs, or connected bank information.
Priority one is the original employer account. Skip payroll submission until login and business selection are settled.
Never provide another person with the owner’s password or authentication code. Employees need payroll records and pay information, not access to the employer’s entire FreshBooks account.
FreshBooks Payroll Setup Takes Planning
FreshBooks says payroll setup usually takes about four business days for approval. Direct-deposit processing can require another four business days, so the first pay date should be at least eight business days after setup begins.
That is not a cosmetic recommendation.
Payroll onboarding includes business information, the Federal Employer Identification Number, bank verification, state tax details, employee information, and authorization documents allowing Gusto to debit payroll funds and pay federal taxes for the employer.
Set up these items before promising a first direct-deposit date:
- legal business information;
- FEIN;
- work locations;
- payroll bank account;
- employee start dates;
- pay schedule;
- state tax registrations;
- signed authorization documents.
FreshBooks says missing the first payroll date selected during onboarding can cause the pay schedule to be updated, with a new first pay date provided. An off-cycle payroll may be needed for missed pay periods.
Start early. Skip choosing a first pay date only a few days away.
Add Employees and Contractors Correctly
Payroll setup begins with a person’s Team Member profile.
For an employee, FreshBooks instructs the owner to open Team Members, select the person, confirm that the role is Employee, and choose Add to Payroll > As an employee. Contractors follow a comparable route using the Contractor role and As a contractor.
An employee and a contractor are not interchangeable labels. The distinction affects tax forms, withholding, payroll calculations, and the information collected during onboarding.
FreshBooks requires businesses adding contractors to acknowledge that the contractor’s Form W-9 will be collected and stored outside FreshBooks.
Do not switch a worker’s classification merely to make setup easier. Worker classification depends on the actual relationship and applicable federal and state law.
FreshBooks documents a specific conversion process. A contractor must first be made inactive before being added as an employee. An employee must be dismissed before being added as a contractor.
Use professional tax or legal advice when classification is uncertain.
Fix “Team Member Info Not Synced”
FreshBooks documents a payroll warning labeled Team member info not synced. It appears when employee information stored between FreshBooks Payroll and Gusto does not match.
The warning does not necessarily block a payroll run, but FreshBooks says it can affect tax calculations and filings.
To correct it:
- Open Team Members.
- Select the affected person.
- Review each Payroll section marked with a red exclamation point.
- Correct or confirm the information.
- Save each section until the warning markers are gone.
Do this before payroll.
A small address discrepancy can have larger consequences because work location, residence, and state details can affect payroll tax treatment. FreshBooks also warns that backdated address changes may trigger automatic payroll adjustments.
Priority two is the red warning marker. Skip assuming the data is harmless because the payroll screen still opens.
Run Payroll Before the Processing Deadline
FreshBooks supports regular payroll, off-cycle payroll, and contractor payments. Regular payroll follows the employer’s established pay schedule.
The documented submission deadline depends on the ACH speed:
- four business days before payday for four-day ACH;
- two business days before payday for eligible two-day ACH;
- submission by 6:30 p.m. Eastern Time on business days.
FreshBooks says the bank debit does not occur until the applicable payroll deadline. Employee direct deposits are scheduled for the payment date displayed during Review and Submit.
Review the displayed date rather than estimating from the calendar.
Weekends and bank holidays can alter the practical processing window. A Friday payday does not mean payroll can always be submitted on Wednesday.
When payroll is being submitted too late for direct deposit, FreshBooks recommends considering check payment and paying employees outside direct deposit.
Do not promise same-day correction. Use the payment method and timing permitted by the current payroll screen.
Why a Payroll Run Will Not Submit
FreshBooks lists several reasons for an error stating that payroll information is required:
- missing or incorrect business information;
- a new signature is required;
- incorrect bank information;
- an employee began working in a new state and additional documents are needed.
Open Payroll settings and inspect any warning banners before editing employee earnings.
A bank-verification problem is not fixed by changing the employee’s hours. A state-tax registration issue is not fixed by running off-cycle payroll repeatedly.
Match the correction to the warning.
FreshBooks also says payroll runs and contractor payments can be canceled only while their status remains Submitted, and cancellation must occur before the 6:30 p.m. Eastern deadline on a business day.
Once the cancellation option disappears, contact FreshBooks support rather than trying to reverse the bank debit manually.
Review Payroll Runs, Stubs, and Reports
FreshBooks keeps payroll and contractor payment history inside the Payroll section. Opening a completed or submitted pay period allows the owner to review pay-period information and supporting records.
Available controls can include:
- Payroll Receipt for the payroll summary;
- employee names for individual pay-stub PDFs;
- contractor payment history;
- cancellation while a run remains eligible;
- payment and debit details.
FreshBooks Payroll account management also includes payroll reports, tax documents, work locations, bank information, state tax details, benefits, and setup documents.
Download the payroll receipt after each run. Skip relying only on the bank withdrawal because one debit may include wages, employer taxes, employee taxes, deductions, or other payroll amounts.
The payroll record explains the bank movement.
How Payroll Taxes Are Handled
FreshBooks Payroll powered by Gusto uses account information supplied by the employer to calculate payroll taxes and submit related payments and filings.
FreshBooks says tax payments are generally made as close to the deadline as possible, allowing time for changes or updates before the filing date.
Automation does not remove the employer’s responsibility to enter accurate information.
Incorrect FEIN details, work locations, employee addresses, prior payroll amounts, or state registrations can affect calculations and filings. Review tax notices and payroll settings rather than assuming every agency letter is automatically resolved.
Historical payroll data deserves particular care. When prior payroll is entered during setup, FreshBooks says Gusto can debit the employer’s bank account for related tax liabilities two days after the first FreshBooks Payroll run.
That debit can surprise a business that expects only the current payroll amount.
Review historical liabilities before the first run. Skip treating the additional bank debit as an unexplained duplicate until payroll tax records have been checked.
Benefits, Deductions, and Employment Changes
Benefits are managed through:
Payroll > More Actions > Payroll Settings > Benefits.
The business can add a benefit, edit its name, and assign employees. Employee deductions are managed inside the person’s Payroll profile under Deductions.
FreshBooks also provides structured dismissal and rehire processes. An employer begins dismissal from the employee’s Payroll area, enters the last employment date, and completes the displayed steps. Rehire uses Begin Rehire and a new start date.
Do not simply make an employee inactive without reviewing final payroll obligations.
Final-pay deadlines, accrued leave, deductions, benefits, and required notices vary by state. FreshBooks provides payroll controls, but the employer remains responsible for following applicable labor and tax rules.
FreshBooks Payroll FAQ
Is FreshBooks Payroll available outside the United States?
The integrated FreshBooks Payroll powered by Gusto product is described for U.S.-based businesses. Availability and eligibility should be confirmed in the account.
How early should I start payroll setup?
FreshBooks recommends a first pay date at least eight business days after setup begins because approval and direct-deposit processing each may require about four business days.
Can employees use the owner’s FreshBooks login?
No. Add them through Team Members and Payroll.
Why does FreshBooks say team information is not synced?
FreshBooks and Gusto contain mismatched employee information. Review every Payroll section marked with a red exclamation point and save the corrected information.
What is the direct-deposit payroll deadline?
FreshBooks lists four business days for four-day ACH or two business days for eligible two-day ACH, submitted by 6:30 p.m. Eastern on business days.
Can I cancel a payroll run?
Only while it remains in Submitted status and before the applicable 6:30 p.m. Eastern business-day deadline.
Why was my bank debited for old payroll taxes?
Historical payroll information can create prior tax liabilities. FreshBooks says Gusto may debit those liabilities two days after the first payroll run.
Where can I find employee pay stubs?
Open the payroll run in Payment History and select the employee’s name in the payment details to download the available PDF.