• What each tool offers
  • Worked example: one $2,400 invoice

Invoicing software with online payments puts a pay option on the invoice, so your client can pay by card, bank transfer or a wallet without you sending bank details. The tools do this in one of two ways:

  • Their own payments service. Square Invoices, PayPal Invoicing, QuickBooks Online with QuickBooks Payments, Wave and Stripe Invoicing process the payment themselves, at the rates on their own fee pages.
  • A payment account you connect. Zoho Invoice and Billed connect to a processor such as Stripe or PayPal. You pay that processor's rates; the invoicing tool may or may not add its own fee.

Which is better for you depends on three things: the fee for the payment method your clients will actually use, whether that method is offered at all, and how long the money takes to reach your bank.

Disclosure: Billed publishes this page, and Billed is one of the tools listed. We haven't ranked, scored or tested the tools. Each product description and rate comes from that vendor's own page, opened on October 29, 2026. Rates change, so check the linked page before you sign up.

What each tool offers

Rates below are US rates for a domestic payment on an invoice, as published on the date above. Subscription prices aren't included; see each vendor's pricing page.

Square Invoices

  • Payment methods: clients can pay an online invoice with a credit card, Apple Pay, Google Pay or ACH bank transfer (Square Invoices). Square also supports recurring invoices with a card on file for auto-billing.
  • Fees: Square's invoice pricing lists online payments at 3.3% + 30¢ on Square Free and 2.9% + 30¢ on Square Plus and Square Premium. In the same page's fee table, "ACH bank transfer (via invoice)" is 1% with a $1 minimum on Square Free, and 1% with a $1 minimum and a $10 fee cap on Square Plus and Square Premium.
  • Payout: "Next day transfers" are listed as included with every plan.

PayPal Invoicing

  • Payment methods: PayPal, Venmo, Apple Pay, credit and debit cards, Pay Later and Pay by Bank (ACH). Clients don't need a PayPal account (PayPal Invoicing).
  • Fees: PayPal's merchant fees page (last updated October 1, 2026) lists separate rates for invoice payments:
    • cards, Apple Pay and other third-party wallets: 2.99% + fixed fee;
    • PayPal Checkout, Venmo or PayPal Guest Checkout: 3.49% + fixed fee;
    • Pay by Bank (ACH): 1%, capped at $10.00 per transaction.
    • The fixed fee for US dollars is 0.49 USD. International invoice payments add 1.50%.

QuickBooks Online with QuickBooks Payments

  • Payment methods: invoices customers can pay online "with card, PayPal, Venmo, Affirm, or Apple Pay", plus ACH bank payments (QuickBooks Payments).
  • Fees: Intuit's payment rates page ("accurate as of 09/18/2026") lists 2.99% for invoices paid by card or digital wallet and 1% for ACH bank payments. Instant deposit is 1.75%.

Wave

  • Payment methods: credit cards, bank payments and Apple Pay through a "Pay now" button on the invoice (Wave Payments).
  • Fees: 2.9% + $0.60 per Visa, Mastercard or Discover transaction and 3.4% + $0.60 per Amex transaction. On the Pro plan, the first 10 card transactions each month are 2.9% + $0 (Wave pricing). Bank payments (ACH/EFT) are 1% per transaction, with a $1.00 minimum fee (Wave Payments).
  • Payout: "1-2 business days for credit card payments and 1-7 business days for bank payments" (Wave Payments).

Stripe Invoicing

  • Payment methods: each invoice links to a Stripe-hosted invoice page that "offers Apple Pay and Google Pay", and Stripe can send reminders when invoices are due or past due (Stripe Invoicing).
  • Fees: Stripe's invoicing pricing is 0.4% per paid invoice on Starter and 0.5% on Plus, and "Stripe Payments pricing will apply". Stripe's US pricing is:
    • domestic cards: 2.9% + 30¢, with 1.5% more for international cards and 1% more if currency conversion is required;
    • ACH Direct Debit: 0.8%, capped at $5.00.
  • Payout: in the US, a card payment made on Monday is available in your Stripe balance on Wednesday, and ACH Debit takes 4 business days (Stripe, balances).

Zoho Invoice

  • How it works: Zoho Invoice connects to payment gateways you set up, including Zoho Payments, PayPal, Stripe, Square, Braintree and Authorize.net (Zoho Invoice help).
  • With Stripe: cards are on by default; you can turn on ACH for customers in the US, Klarna and Apple Pay. "Zoho does not charge any additional fees"; Stripe's pricing applies (Zoho, Stripe).

FreshBooks

  • FreshBooks Payments powered by Stripe is "only available for businesses in Canada and the United States". Clients can pay by debit card, credit card or ACH bank transfer. The fees are on FreshBooks' own transaction fee list, and there are no setup, monthly or cancellation fees (FreshBooks support).
  • Outside the US and Canada, FreshBooks says businesses can use Stripe Standard instead, at Stripe's fees (FreshBooks support).

Billed

Worked example: one $2,400 invoice

These are sample figures. A US consultant invoices a US client for $2,400. Here is what each tool's published rate takes from that one payment.

Paid by card (fee, then what you receive):

  • Square Free (3.3% + 30¢): $79.50, you get $2,320.50
  • Square Plus (2.9% + 30¢): $69.90, you get $2,330.10
  • PayPal Invoicing, card (2.99% + 49¢): $72.25, you get $2,327.75
  • PayPal Checkout or Venmo (3.49% + 49¢): $84.25, you get $2,315.75
  • QuickBooks Payments (2.99%): $71.76, you get $2,328.24
  • Wave (2.9% + 60¢): $70.20, you get $2,329.80
  • Your own Stripe account, e.g. through Zoho Invoice or Billed (2.9% + 30¢): $69.90, you get $2,330.10
  • Stripe Invoicing Starter (2.9% + 30¢, plus 0.4%): $79.50, you get $2,320.50

Paid by bank transfer (ACH):

  • Square Free (1%, $1 minimum): $24.00, you get $2,376.00
  • Square Plus or Premium (1%, $10 cap): $10.00, you get $2,390.00
  • PayPal Pay by Bank (1%, $10 cap): $10.00, you get $2,390.00
  • QuickBooks ACH (1%): $24.00, you get $2,376.00
  • Wave (1%): $24.00, you get $2,376.00
  • Stripe ACH Direct Debit (0.8%, $5 cap): $5.00, you get $2,395.00

What the example shows:

  • The payment method matters more than the tool. Card fees on this invoice range from $69.90 to $84.25. Every bank option costs less than every card option, from $5.00 to $24.00.
  • Caps decide large invoices. PayPal, Square Plus and Premium, and Stripe cap their bank fees, so they stay at $10.00, $10.00 and $5.00 however large the invoice. Square Free, QuickBooks and Wave list 1% with no cap, which is $24.00 here and grows with the invoice.
  • Fees stack when the invoicing tool has its own. Stripe Invoicing's 0.4% adds $9.60 to the card fee here. Zoho Invoice and Billed say they add nothing to Stripe's rates.
  • Not every client can pay by bank. If your clients pay by card anyway, compare the card rates, and look at what your typical client uses before you choose.

The invoice shows as paid in full, but your bank receives the net amount. Record the fee as a payment processing expense so your books match the deposit. For ways to lower the card cost, see how to reduce payment processing fees.

What to check before you choose

  • The methods your clients will see. Card only, or bank transfer and wallets too? If bank transfer is offered, is it limited by country? Zoho Invoice's Stripe ACH is for US customers; FreshBooks Payments is for businesses in the US and Canada.
  • The rate for each method, on the vendor's own fee page, for your country. The rates above are US rates.
  • Whether the invoicing tool adds a fee on top of the processor's, as Stripe Invoicing does.
  • How fast money reaches your bank. Payout times differ by method: Wave lists 1–2 business days for cards and 1–7 for bank payments, and Stripe lists 2 business days for US card payments and 4 for ACH Debit.
  • Whether the invoice is marked paid for you. If it isn't, you'll match deposits to invoices by hand.
  • Recurring billing, if you bill the same clients every month: recurring invoices with a stored payment method save chasing.

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Frequently Asked Questions

Which invoicing software has online payments built in?

Square Invoices, PayPal Invoicing, QuickBooks Online with QuickBooks Payments, Wave and Stripe Invoicing all process invoice payments themselves. FreshBooks does too through FreshBooks Payments, for businesses in the US and Canada. Zoho Invoice and Billed take payments through a processor you connect, such as Stripe or PayPal.

What is the cheapest way to get an invoice paid online?

On a large US invoice, a bank payment with a capped fee. On a $2,400 sample invoice, Stripe's ACH Direct Debit costs $5.00 (0.8%, capped at $5), and PayPal's Pay by Bank and Square's ACH on its Plus or Premium plan cost $10.00 (1%, capped at $10), while card payments cost about $70 to $84. Bank payments are only cheaper if your client is willing and able to pay that way.

Do invoicing tools charge extra on top of the payment processor?

It depends on the tool. Stripe Invoicing adds 0.4% or 0.5% per paid invoice on top of Stripe's payment pricing. Zoho Invoice says it charges no additional fees on Stripe payments, and Billed adds no markup on Stripe or PayPal payments. Tools with their own payments service, such as Square, PayPal, QuickBooks Payments and Wave, publish their own rate for each payment method, and at Square and Wave the rate can depend on your plan.

How long does an online invoice payment take to reach my bank?

It depends on the tool and the payment method. Wave lists 1–2 business days for card payments and 1–7 for bank payments. Square lists next day transfers. In the US, Stripe makes card payments available after 2 business days and ACH Debit after 4, then pays out on your payout schedule.

Can clients pay an invoice without a PayPal or Square account?

Yes. PayPal says customers can pay its invoices even without a PayPal account, and Square Invoices can be paid by card, Apple Pay, Google Pay or ACH bank transfer. Billed says clients pay by card through Stripe without creating an account.

Are online payment fees the same outside the US?

No. The rates on this page are the vendors' US rates. Card, bank and international fees differ by country, so open each vendor's fee page for the country your business is in.

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