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Bill Your Customers Easily Using QuickBooks and ACH Pro

  • Ian Berryman
  • Aug 6
  • 3 min read

Updated: Sep 8

ACH debits billing multiple accounts

If your business uses QuickBooks for invoicing and accounting, you already have a solid system for tracking who owes what. But when it comes time to actually collect those payments, are you still waiting on paper checks or paying steep fees for online payments?


ACH Pro helps you bridge the gap — making it easy to collect payments from your QuickBooks customers using ACH (Automated Clearing House) transfers through your existing bank. It’s faster, cheaper, and integrates seamlessly into your existing workflow.


Why Use ACH for Billing?

ACH payments are:

  • Much cheaper than credit cards (no 2–3% processing fees)

  • Faster than waiting for checks in the mail since you control the payment process

  • Safer and easier to reconcile

  • Preferred by many customers who want recurring billing or autopay


And here’s a key reason many businesses process ACH through their existing bank:

QuickBooks charges 1% for ACH invoice payments. Most banks charge a flat fee between $0.10 - $0.50

With ACH software like ACH Pro, you pay a flat monthly rate and send the payments through your existing bank. That means:

  • No 1% fee on invoice payments

  • No dependency on QuickBooks’ built-in payment processor

  • Better margins on every dollar collected

  • Quicker funds availability


Example: A $10,000 invoice collected via QuickBooks ACH will result in a $100 fee. The same $10,000 collected using ACH Pro and your bank would likely cost $0.10–$0.50 total.


How ACH Pro Works with QuickBooks

ACH Pro integrates with your QuickBooks data (either Desktop or Online) and allows you to:

  1. Sync customer information automatically

  2. Manage authorizations so you stay compliant

  3. Find open invoices in QuickBooks

  4. Generate a NACHA file that instructs your bank to debit the customer and credit your account


Step-by-Step: Billing with ACH Pro and Your Bank


Walk through the steps in this live demo. (This demo covers accounts payable but the steps are the same for billing)


Step 1: Contact Your Bank

Ask your bank to enable NACHA file upload access on your business account. Your bank may require an application or review process so it's a good idea to start this conversation first.


Step 2: Gather Bank Info and ACH Authorizations

For each customer you plan to debit via ACH:

  • Collect their routing number, account number, and account type

  • Get a signed ACH authorization form


Note: ACH Pro can help you securely collect bank info and authorizations from your customers in one step.


Step 3: Find invoices in QuickBooks

ACH Pro connects directly to QuickBooks so you can search for open invoices and select the ones you want to bill.

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Step 4: Review and Generate the NACHA File

ACH Pro will convert your QuickBooks invoices into ACH transactions automatically and provide you with a NACHA formatted file.


Step 5: Upload the File to Your Bank

Submit the NACHA file through your bank’s ACH portal. Most banks provide next-day posting, so you can upload a file on Monday that should post on Tuesday to both your account and your customers' accounts.


Pro Tips

  • Offer ACH as a preferred or discounted payment method to encourage adoption, remember that you're no longer losing 2-3% on cards payments and can pass this along as an incentive if desired

  • Use recurring billing in QuickBooks to automatically collect from repeat customers

  • Include invoice numbers in the addenda for easier reconciliation

  • Use prenotes to verify account info before the first debit

  • Maintain all authorization records in case of dispute


Final Thoughts

Billing your QuickBooks customers using ACH is one of the easiest ways to get paid faster, lower your costs, and reduce friction for both you and your clients.

ACH Pro makes the process simple, compliant, and reliable — whether you’re collecting from one customer or hundreds. And unlike QuickBooks’ built-in billing system, you won’t pay 1% per transaction.


Get Started with ACH Pro

ACH Pro helps you turn QuickBooks invoices into clean, compliant NACHA files in just minutes — no technical expertise required.


  • Works with QuickBooks Desktop or Online

  • Securely store your recipients information

  • Works with any U.S. bank that accepts NACHA files


Try ACH Pro Free and start collecting ACH payments the smarter way.



 
 
 
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