How to set up payment methods on FreshBooks

beginner 8 min read Updated 2026-03-18

Quick Answer

Setting up payment methods in FreshBooks involves accessing the Payments section in Settings, connecting your bank account, and configuring payment gateways like Stripe, PayPal, or FreshBooks Payments. This enables clients to pay invoices directly through multiple payment options.

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Prerequisites

Active FreshBooks account
Business bank account information
Credit card processing account or PayPal business account
Business verification documents

Step-by-Step Instructions

Access Payment Settings

Log into your FreshBooks account and click on Settings in the left sidebar. From the dropdown menu, select Payments to access your payment configuration options.

Make sure you have admin privileges on the account to modify payment settings.

Set Up FreshBooks Payments

In the Payments section, click Get Started under FreshBooks Payments. Fill out your business information including legal business name, address, and tax ID. Upload required documents such as a voided check or bank statement for verification.

FreshBooks Payments typically has the lowest processing fees and fastest setup time.

Connect Your Bank Account

Click Connect Bank Account and enter your routing number and account number. Verify the micro-deposits that FreshBooks will send to your account within 1-2 business days by entering the amounts in the Verify Account section.

Use a dedicated business checking account rather than a personal account for better financial organization.

Configure Additional Payment Gateways

To add PayPal, click Connect PayPal and sign in to your PayPal business account. For Stripe integration, click Connect Stripe and authorize the connection. Each gateway will require you to complete their respective verification processes.

Offering multiple payment methods can increase your invoice payment rates by up to 40%.

Set Payment Terms and Fees

Under Payment Settings, configure your default payment terms, late fees, and processing fee handling. Choose whether to absorb processing fees or pass them to clients by toggling Add processing fees to invoices.

Enable Online Payments for Invoices

Go to Settings > Invoice Customization and ensure Online Payments is enabled. This will automatically add payment buttons to your invoices. You can customize which payment methods appear by checking the boxes next to each option.

Test the payment process by sending yourself a test invoice to ensure everything works correctly.

Configure Automatic Payment Reminders

In Settings > Automation, set up automatic payment reminders by clicking Create Automation. Choose when to send reminders (3 days overdue, 7 days overdue, etc.) and customize the email templates for each reminder.

Gentle, professional reminders sent 3-5 days after due date typically have the highest success rate.

Common Issues & Troubleshooting

Bank account verification fails

Double-check your routing and account numbers for accuracy. Contact your bank to ensure the account accepts ACH transfers. If micro-deposits don't arrive within 3 business days, contact FreshBooks Support for assistance.

PayPal or Stripe connection issues

Ensure you're using a business account (not personal) for both services. Clear your browser cache and try connecting in an incognito window. Verify that your PayPal or Stripe account is in good standing and not restricted.

Clients can't see payment buttons on invoices

Check that Online Payments is enabled in Settings > Invoice Customization. Ensure at least one payment method is active and verified. Send a test invoice to yourself to confirm payment buttons appear correctly.

Processing fees not calculating correctly

Verify your fee structure in Settings > Payments > Processing Fees. Make sure the Add processing fees to invoices toggle matches your preference. Contact your payment processor if fees don't match their published rates.

Prices mentioned in this guide are pulled from current plan data and may change. Always verify on the official FreshBooks website before purchasing.

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