QuickBooks + BTCPay Server: self-custody Bitcoin invoicing | payinbtc.me

QuickBooks is the default ledger for American small business. Intuit reported roughly 10 million QuickBooks customers, about 6.5 million of them on QuickBooks Online, and independent market estimates put its share of US small business accounting software above 80 percent. Invoicing inside it is thorough: recurring invoices, progress billing, sales tax, and a payments layer that takes cards and bank transfers. What it does not have is a way to accept Bitcoin.

The payments layer is also where the cost sits. QuickBooks Payments currently charges 2.99 percent on invoiced card payments, 3.5 percent on keyed-in cards, and 1 percent on ACH bank transfers. (based on 2024 figures). On a four-figure invoice that is a meaningful slice of the margin, taken on money you have already earned, and every business owner who has looked at a merchant statement knows the number keeps growing with revenue.

PayInBTC.me connects QuickBooks to BTCPay Server so a Bitcoin option appears on the invoices you already send. BTCPay Server is free, open source, and self-hosted, and it charges nothing beyond Bitcoin network fees. The customer pays over Lightning or on-chain, the Bitcoin lands in the wallet you control, and nothing about your QuickBooks workflow changes.

Why QuickBooks and BTCPay Server work together

The fee QuickBooks cannot remove

Every payment method QuickBooks offers natively carries a percentage. Cards run at 2.99 percent through QuickBooks Payments, keyed-in cards at 3.5 percent, and even ACH takes 1 percent. BTCPay Server takes no cut at all, because it is software you run rather than a processor you sign up with, so the only cost on the payment itself is the Bitcoin network fee. PayInBTC.me charges a flat rate in sats per invoice, not a share of the amount, which means the cost of accepting a 500 dollar invoice and a 50,000 dollar invoice is the same.

Open source software, not a merchant account

BTCPay Server is MIT licensed and has been developed in the open since 2017, with funding from grant programs rather than transaction revenue. There is no account application, no underwriting, and no provider that can freeze a balance or close you down for being in an industry it dislikes. For a business that has ever had a payment processor decide it was too risky, that difference is the whole argument, and it is the reason many QuickBooks users who look at Bitcoin end up looking at BTCPay first.

Hosted BTCPay if you do not want to run a server

Self-hosting BTCPay means running a Bitcoin node, keeping it patched, and staying online. Plenty of businesses would rather not. PayInBTC.me offers a hosted BTCPay Server add-on at 2,500 sats per month or 25,000 sats per year: we run the infrastructure, the updates, the monitoring, and the daily backups, and payments still settle directly to your own wallet. You get the self-custody without the sysadmin work, and you can move to your own instance later without changing anything in QuickBooks.

Read-only on the QuickBooks side

PayInBTC.me connects to QuickBooks with read-only access. It reads the invoice number, amount, and currency to build the payment, and it never writes to your books. Your chart of accounts, invoice templates, numbering, and sales tax handling stay exactly as your bookkeeper set them up. The Bitcoin side runs entirely through BTCPay Server, which never sends anything back into QuickBooks either.

How the integration works

Setup takes about five minutes if you already have a BTCPay Server instance, and needs no crypto knowledge. Once connected, the flow runs on its own for every invoice you enable it on.

Connect QuickBooks and BTCPay Server

Sign in to PayInBTC.me, authorize QuickBooks through OAuth, and point the connection at your BTCPay Server instance using its store API key. The QuickBooks side is read-only, so PayInBTC.me can see invoice details but cannot change your books. If you do not run BTCPay yourself, the hosted add-on gives you an instance to connect to.

Add the Bitcoin link to an invoice

A 'Pay with Bitcoin' link is placed on the QuickBooks invoices you choose. Your template, logo, invoice numbering, and payment terms stay as they are, and customers who want to pay by card or ACH still can.

Customer chooses to pay in Bitcoin

When the customer clicks the link, PayInBTC.me fetches the invoice total from QuickBooks, calculates the Bitcoin amount at the live exchange rate, and redirects to your BTCPay Server checkout.

Payment settles to your wallet

BTCPay Server presents a Lightning invoice for smaller amounts and an on-chain address for larger ones, depending on how you have configured the store. The Bitcoin goes straight to the wallet or node you control. PayInBTC.me never touches the funds.

You get a confirmation and mark the invoice paid

PayInBTC.me emails you when the payment clears, and BTCPay Server records the invoice with the exchange rate at the moment of payment. You then mark the invoice paid in QuickBooks yourself, since the connection does not write back.

What US businesses get from this pairing

No percentage taken from the invoice

BTCPay Server charges no processing fee, and PayInBTC.me bills a flat amount in sats regardless of invoice size. Compared with 2.99 percent on an invoiced card payment, the saving grows with every larger job you bill.

Bitcoin under your own keys

Settlement is non-custodial. Payments go from the customer to your BTCPay Server and into the wallet you control, with no processor holding a balance and no payout schedule to wait on.

No account that can be closed

BTCPay is software rather than a merchant account, so there is no underwriting, no KYC gate on the payment layer itself, and no risk team deciding your industry is no longer welcome.

No chargebacks

A confirmed Bitcoin payment stays confirmed. For US businesses that bill new clients or ship before final payment, removing card chargeback exposure removes a real category of loss.

Lightning for speed, on-chain for size

BTCPay Server supports Lightning through LND, Core Lightning, and Eclair, alongside on-chain payments. Small invoices clear in seconds, larger ones can settle on-chain where finality matters more than speed.

Records that hold up at tax time

BTCPay Server logs each invoice with the fiat rate applied at the time of payment, which pairs with the invoice record in QuickBooks. The IRS treats Bitcoin as property, so that rate is what your accountant will need. This is not tax advice, and your accountant should confirm the treatment for your entity.

What it costs on a typical invoice

Take a 2,500 dollar invoice, a common size for a US agency, contractor, or professional services firm billing a project milestone. Here is roughly what each payment method costs you.

Method	Cost on a $2,500 invoice	Notes
Card via QuickBooks Payments	About $74.75	2.99% on invoiced card payments, 3.5% if the card is keyed in.
ACH bank transfer	About $25	1% per transfer, slower to clear and still manual to chase.
Bitcoin via PayInBTC.me and BTCPay Server	About $1.50	Flat 1,500 sats per invoice on pay-per-use. BTCPay Server charges no processing fee; the customer pays the Bitcoin network fee

On this one invoice the difference is roughly 73 dollars. A firm sending twenty invoices of this size a year is looking at close to 1,500 dollars in card fees against about 30 dollars in flat charges, or 25 dollars a year if you take the unlimited annual plan.

Who this fits

US agencies and consultancies billing four and five figures

Studios, dev shops, and professional services firms where a single invoice can carry 75 dollars or more in card fees. A flat sats charge changes the math on every project invoice, and the QuickBooks side of the workflow stays untouched.

Businesses that already run BTCPay Server

Merchants using BTCPay for a WooCommerce or Shopify storefront usually have no equivalent for the invoices they send from QuickBooks. This connects the same instance and the same wallet to that side of the business.

Owners who want to hold part of revenue in Bitcoin

If Bitcoin on the balance sheet is a deliberate choice rather than a novelty, non-custodial settlement into your own node means the treasury position starts the moment the customer pays, with no processor converting or holding it first.

Firms in industries payment processors treat as risky

Businesses that have had a merchant account reviewed, held, or closed get a payment route that does not depend on anyone's approval, because BTCPay Server is software they run rather than a service that can drop them.

Getting started

You need a QuickBooks account and a BTCPay Server store. If you do not want to run BTCPay yourself, the hosted add-on covers it.

Set up a BTCPay Server store and connect the wallet you want payments to settle to, or add the hosted BTCPay Server option at PayInBTC.me.
Register at payinbtc.me, authorize QuickBooks, and paste your BTCPay Server store API key.
Enable the Bitcoin payment link on the invoices you want to offer it on, then send one to yourself as a test before it goes to a customer.

The first month is free, so you can run real invoices through the setup before deciding whether it stays. Full setup instructions are at docs.payinbtc.me.

Get started free →

Frequently Asked Questions

Does this change how I create invoices in QuickBooks?

No. You invoice in QuickBooks exactly as you do now. PayInBTC.me adds a 'Pay with Bitcoin' link to the invoices you choose and reads the invoice details to build the payment. Templates, numbering, sales tax, and your chart of accounts stay as they are, and card and ACH remain available to customers who prefer them.

Do I have to run my own BTCPay Server?

Not necessarily. If you already run BTCPay Server, you connect your existing store with its API key. If you would rather not manage a node, PayInBTC.me offers a hosted BTCPay Server add-on at 2,500 sats per month or 25,000 sats per year, where we handle the servers, updates, monitoring, and backups while payments still settle to your own wallet.

Does the payment only work over the Lightning Network?

No. BTCPay Server supports both Lightning and on-chain Bitcoin, and the options your customer sees depend on how your store is configured. Lightning suits smaller invoices that should clear in seconds, while on-chain is the usual choice for larger amounts.

Where does the Bitcoin end up?

In the wallet you control. BTCPay Server is non-custodial by design, so Bitcoin goes from the customer to your own node and wallet. PayInBTC.me reads your QuickBooks invoice data and passes the payment request through, but it never holds or routes the funds.

Do I need to understand Bitcoin to use this?

For the payment flow, no. Your customer handles the Bitcoin side when they pay, and you receive an email when it clears. You do need a wallet to receive to, and if you self-host BTCPay Server you are running a piece of infrastructure, which is why the hosted option exists for businesses that would rather skip that part.

Will paid invoices be marked as paid automatically in QuickBooks?

Not yet. PayInBTC.me has read-only access to QuickBooks and does not write back to it, so you mark the invoice as paid yourself after the confirmation email arrives. Automatic reconciliation is on the roadmap.

What does it cost per invoice?

PayInBTC.me charges a flat 1,500 sats per invoice on pay-per-use, or 2,500 sats per month for unlimited invoices, or 25,000 sats per year. The first month is free, with three free invoices on pay-per-use. BTCPay Server itself is free and open source and takes no percentage, so the only other cost is the Bitcoin network fee.

Does this work outside the United States?

Yes. There are no geographic restrictions on the PayInBTC.me connection, and BTCPay Server is software you host, so it is not tied to a country list the way a licensed processor is. QuickBooks Online sells country editions in the US, Canada, the UK, Australia, and elsewhere, and the integration reads invoices the same way in each. Check your local rules on accepting and reporting Bitcoin before you start.

More questions? See our full FAQ →

Accept Bitcoin on QuickBooks Invoices with BTCPay Server