By Melissa Turner, payment-operations support lead with 9 years of experience handling invoice disputes and merchant payout reviews
Last reviewed: July 22, 2026
FreshBooks business owners sign in to review online payments, payout activity, refunds, and client chargebacks. A chargeback is opened through the client’s bank, so it cannot be resolved by deleting the invoice or changing its payment status inside FreshBooks.
This independent guide is not affiliated with FreshBooks.
Act on the dispute notice first. Skip routine invoice edits until the response deadline, disputed transaction, and available evidence have been confirmed.
What a FreshBooks Chargeback Means
FreshBooks Payments is an online payment service powered by Stripe for eligible accounts in the United States and Canada. A client chargeback, also called a dispute, begins when the client asks their bank or card issuer to question a payment shown on their statement.
The card issuer, not FreshBooks, makes the final decision.
Once a dispute opens, the original payment is reversed while the claim is reviewed. FreshBooks states that the disputed amount and a separate nonrefundable $15 dispute fee are deducted from the merchant’s FreshBooks Payments balance. When that balance is insufficient, funds may be withdrawn from the connected bank account.
This is different from a normal refund.
A refund is initiated by the business. A chargeback is initiated by the client through their financial institution.
Use the Correct FreshBooks Route
| Your task | Correct starting point |
|---|---|
| Enter the business account | FreshBooks login |
| Review online transactions | Payments > Online Payments |
| Open payment and dispute details | FreshBooks Payments Stripe dashboard |
| Respond to a chargeback | Respond to Dispute or Go to Stripe |
| Accept the dispute | Dispute record in the Stripe dashboard |
| Check payout balances | Online Payments and Payout History |
| Refund an eligible payment | Invoice or Payments section |
| Reach account support | Help Centre and FreshBot |
FreshBooks lists online transactions with statuses including Succeeded, Declined, Pending, Refunded, and Charged Back. A charged-back payment is or was involved in the dispute process.
Do this first: find the exact transaction. Skip searching only by the invoice total because one payout can contain several client payments.
Log In and Open the Right Business
FreshBooks supports direct email and password access, Google sign-in, and Apple sign-in. Direct FreshBooks login may also require a six-digit code when two-factor authentication is enabled.
Users with several businesses must select the correct business after authentication. This small step matters when the same owner accepts payments under multiple companies or brands.
A valid login can lead to the wrong ledger.
Check the business name, client, invoice number, transaction date, and payment amount before responding to a dispute. Do not create a second account because a payment appears missing; another account will not contain the established transaction or dispute history.
FreshBooks says its emailed 2FA code remains valid for 10 minutes. Selecting Remember this device can keep the device recognized for 30 days, although browser updates, operating-system changes, and some extensions can cause it to be treated as new.
Priority one is access. Skip payout or dispute changes until the original account is open.
Find the Charged-Back Transaction
The documented FreshBooks route is:
Payments > Online Payments
The Online Payments area includes invoice payments and checkout-link payments. Filters can narrow the list by transaction status, date, client, source invoice, and other payment details.
For a dispute, look for Charged Back.
FreshBooks records won and lost disputes differently:
- After a won dispute, another transaction with Paid status appears.
- After a lost dispute, the original transaction remains Charged Back.
- A lost dispute also changes the related invoice status to Declined.
Do not manually add another payment merely because the invoice changed to Declined. The dispute workflow may create the correct replacement payment automatically if the bank later rules in the business’s favor.
Check the history first.
Respond Before the Deadline
FreshBooks says merchants generally receive a limited response window of 7 to 21 days. The exact deadline belongs to the individual dispute and should be read from the notice or Stripe dashboard rather than estimated from the email date.
The response route is:
- Open Respond to Dispute from the notification email, or select Go to Stripe from the FreshBooks dashboard banner.
- Enter the connected FreshBooks Payments Stripe account.
- Open Disputes.
- Select the affected payment.
- Choose Counter Dispute or Accept Dispute.
Countering means the business disputes the client’s claim and submits supporting evidence. Accepting closes the case without contesting the chargeback.
There is one evidence submission opportunity. FreshBooks warns that submitted evidence cannot be updated after the dispute reaches Submitted status.
Review every item before sending.
Evidence for a FreshBooks Dispute
Evidence should answer the reason given by the card issuer. A generic collection of documents is less useful than records that directly address the client’s specific allegation.
FreshBooks identifies examples such as:
- signed contracts or statements of work;
- delivery tracking for physical goods;
- signed work-completion records for services;
- client communications acknowledging the work or invoice;
- refund and cancellation terms accepted at purchase;
- FreshBooks activity showing that the client viewed or paid the invoice.
For a “product not received” claim, delivery or completion evidence matters. For “duplicate,” the business needs to show that separate charges represented separate transactions or that only one successful charge occurred. For an “unrecognized” claim, records connecting the client to the order and a recognizable statement descriptor can matter.
Do not submit unrelated personal information. Provide only records necessary to establish the transaction, authorization, delivery, or agreed terms.
Priority two is relevance. Skip quantity and focus on the dispute reason.
Common Chargeback Reasons
FreshBooks lists several dispute categories:
Credit Not Processed: The client claims an expected refund or credit was not received.
Duplicate: The client says the same transaction was charged more than once.
Fraudulent: The cardholder denies authorizing the payment.
Incorrect or General: The client disputes the charged amount or raises a claim not covered by another category.
Product Not Received: The client says the goods or services were not delivered.
Product Unacceptable: The client says the result differed from what was promised.
Subscription Canceled: The client claims billing continued after cancellation.
Unrecognized: The client does not recognize the business name shown on the statement.
An unfamiliar statement descriptor can create avoidable confusion. FreshBooks lets eligible businesses review or edit payment information, including the descriptor clients may see, through Online Payments settings and the connected Stripe dashboard.
Use a recognizable business identity. Skip abbreviations that clients would not connect with the invoice sender.
What Happens After Evidence Is Submitted
Stripe transfers the submitted evidence to the issuing bank. FreshBooks says the issuer may take 30 to 75 days to review it, while the full dispute lifecycle can extend to roughly two or three months.
No outcome is assured.
When the business wins, the transaction amount is returned, but the card network retains the nonrefundable dispute fee. A new Paid transaction and invoice payment entry are created.
When the business loses, the disputed funds remain returned to the client, the fee remains charged, and the invoice is marked Declined.
Do not invoice the client again automatically while the case remains under review. Whether the business has a separate contractual right to pursue payment can depend on the agreement and local law.
Use legal advice for material collection decisions.
ACH Disputes Work Differently
FreshBooks states that successful bank-transfer disputes are final and cannot be appealed through the credit-card evidence process. The business must work directly with the client if the transfer was disputed by mistake.
FreshBooks identifies common ACH dispute grounds using rules associated with the National Automated Clearing House Association (NACHA), including:
- the debit was never authorized or authorization was revoked;
- the debit was processed earlier than authorized;
- the amount differed from the authorized amount.
This is a substantial difference.
Do not follow credit-card chargeback instructions for an ACH dispute. Confirm the payment method before planning a response.
Chargebacks Can Pause Payouts
A client payment and a bank payout are separate events. FreshBooks batches processed online payments into payouts that move funds to the connected bank account.
Refunds and chargebacks can reduce the available balance. FreshBooks says payouts may be paused when the payment account has a negative balance, when a reserve is being held to cover potential refunds or disputes, or when the account is under a risk or compliance review.
The Payout History area shows:
- payout date;
- destination account’s last four digits;
- delivery method;
- status;
- fees;
- amount.
A negative payout amount can represent a withdrawal used to cover a negative payment balance.
Do not assume the connected bank was charged twice. Compare the chargeback, payment balance, and payout timeline.
Refund or Chargeback?
Use a refund when the business agrees that money should be returned and the payment remains eligible for the supported refund workflow. FreshBooks currently allows owners and admins to refund many card payments up to 60 days old and ACH payments up to 90 days old from the account. Older transactions may require another support route.
Use the dispute workflow after the client has already opened a chargeback through their bank.
Refunding outside the dispute record does not necessarily close a chargeback already in progress. It can create additional reconciliation work if both processes continue.
Check the payment status before acting.
FreshBooks says PayPal refunds must be handled manually through PayPal and then reflected in FreshBooks.
Payment routes vary by processor and region.
Contact FreshBooks Support
Signed-in users can open the FreshBooks support page, select Ask Us, enter “contact support,” and follow FreshBot’s instructions. Regional phone options may also appear based on account, region, plan, and request time.
Users who cannot log in can select Contact Us from the Help Centre and follow the FreshBot support route without entering the account first.
Prepare:
- the affected invoice number;
- payment method;
- transaction status;
- dispute deadline;
- payout status;
- concise non-sensitive error wording;
- whether the issue affects one payment or several.
Do not include account credentials or unnecessary client financial information.
FreshBooks FAQ
Is a chargeback the same as a refund?
No. The client starts a chargeback through their bank; the business starts a refund.
How long do I have to answer a chargeback?
FreshBooks says the response window is generally 7 to 21 days, but the deadline displayed for the individual case controls.
Can I edit dispute evidence after submitting it?
No. FreshBooks states that evidence cannot be updated after the dispute reaches Submitted status.
Who decides whether I win?
The client’s issuing bank makes the final decision. Stripe transfers the merchant’s evidence, while FreshBooks provides the invoicing platform and status notices.
How long can a decision take?
The bank’s evidence review may take 30 to 75 days, and the full case can last roughly two or three months.
Is the dispute fee returned when I win?
No. FreshBooks says the transaction amount is returned after a win, but the separate dispute fee remains nonrefundable.
Can I appeal an ACH dispute?
No. FreshBooks says successful bank-transfer disputes are final. The business must work directly with the client if the transfer was disputed in error.
Why did my payout become smaller or pause?
A refund, chargeback, reserve, negative balance, verification request, or risk review can reduce or pause payouts. Review the FreshBooks Payments balance and payout timeline before changing bank settings.