Best Invoicing Software for Small Business: Prices and Payment Fees

Sending an invoice is the cheap part. Wave, Zoho Invoice, Square and PayPal let you send invoices for $0 a month, and the paid tools start around $19 to $38. The real cost comes when the client pays: a card payment on an invoice costs close to 3% at every vendor here, while an ACH bank transfer costs 1% or less, sometimes with a cap. On $10,000 a month of invoices, the processing fees are several times the subscription.

Here is what each tool charges to send invoices and to collect the money, taken from each vendor's own US pricing pages.

The invoicing tools at a glance

The card rates are for US cards. Clients paying with a foreign card cost more: Stripe adds 1.5%, and PayPal adds 1.50% to any payment from an international invoice.

What ten invoices a month really cost

Take a business that sends ten $1,000 invoices a month. Five clients pay by card and five by ACH. Here is the monthly bill at each tool, subscription included.

The spread is under $50 a month, and most of it is the subscription. The fees themselves barely move: card payments cost $145 to $167 everywhere. Two things change the picture far more than the tool you pick:

• How your clients pay. If all ten clients paid by card, fees would be about $290 or more at any vendor. If all ten paid by ACH, they would be $100 at 1%, or $50 at Stripe's capped rate (before its $40 Invoicing fee).
• How big your invoices are. The ACH caps only matter on large invoices. A single $5,000 invoice paid by ACH costs $50 at QuickBooks, FreshBooks, Wave or Square Free, $10 at PayPal or Square Plus, $9 at Xero (Stripe ACH debit) and $5 at Stripe (plus Stripe's $20 Invoicing fee).

If you invoice a few large B2B clients, a capped ACH rate saves real money. If you invoice many small jobs paid by card, pick on features and subscription price.

Wave: best free invoicing with bookkeeping

Wave's Starter plan is $0 and includes unlimited estimates, invoices, bills and bookkeeping records. You pay only when a client pays online: 2.9% + $0.60 per card payment (3.4% + $0.60 for Amex) and 1% per bank payment, with a $1 minimum. Wave says card payments arrive within 1 to 2 business days and bank payments within 1 to 7.

Wave Pro costs $19 a month or $190 a year. For invoicing, its main benefit is that the $0.60 fixed fee is waived on your first 10 card payments each month, after which Starter rates apply. Pro also adds automatic bank transaction import.

What to watch:

• The $0.60 fixed fee is double the usual 30¢. It adds up on many small invoices: on a $50 invoice the card fee is $2.05, or 4.1%.
• No cap on ACH. A $5,000 bank payment costs $50.
• Instant payout costs 1% extra (minimum $1) if you want card money in minutes.

Choose it if you want invoicing and basic books in one free tool and send a modest number of invoices. If mileage, receipts and tax categories matter more to you than invoices, see bookkeeping software for freelancers.

Zoho Invoice: best free tool if you choose your own gateway

Zoho Invoice is free. The free plan allows up to 2 users, 500 invoices a year and 3 projects. There is no paid tier: for subscriptions and more advanced billing, Zoho points you to Zoho Billing.

Zoho says it "does not charge any additional fees for the payments you receive". You connect a payment gateway such as Stripe, PayPal, Square, Authorize.net or Braintree, and that gateway's own fees apply. With Stripe, for example, US cards cost 2.9% + 30¢.

What to watch:

• 500 invoices a year is about 42 a month. A business sending more needs another tool.
• Two separate accounts. You manage your gateway account (and its fees, payouts and disputes) outside Zoho.

Choose it if you send a few dozen invoices a month and want a free invoicing tool without taking on a new payment processor's rates.

QuickBooks Online: best if your accountant works in QuickBooks

QuickBooks Online has a Free plan for 1 user that sends up to two invoices a month, or unlimited invoices if you qualify for and turn on QuickBooks Payments. The paid plans are full accounting software (compared with Xero, FreshBooks and Wave in QuickBooks alternatives):

Intuit currently offers 50% off for the first three months on paid plans.

QuickBooks Payments charges 2.99% for a card or digital-wallet payment on an invoice, with no fixed fee, and 1% for ACH, with no minimum or cap listed. There is no monthly payments fee.

What to watch:

• No ACH cap. Large bank payments cost a full 1%.
• You pay for accounting you may not need if invoicing is the only job.

Choose it if you want your invoices, payments and books in the software your accountant already uses.

FreshBooks: best for billing clients for your time

FreshBooks is built around client work: time tracking, estimates, proposals and retainers. Its plans are priced by the number of billable clients you can invoice:

FreshBooks Payments, or Stripe connected to FreshBooks, charges 2.9% + $0.30 per card payment and 1% for ACH bank transfers. Select, the custom plan, lists lower card fees and capped ACH fees, without publishing the numbers. FreshBooks currently shows 80% off for four months on the monthly plans.

What to watch:

• The client limit. Lite covers 5 billable clients, so most small businesses land on Plus.
• Extras are add-ons. Team members cost $11 a month each, and Advanced Payments is $20 a month.

Choose it if you bill a manageable list of clients for hours and projects, as consultants, designers and agencies do. Law firms that bill from trust accounts need more than this: see legal billing software.

Xero: best for a growing business with several people in the books

Xero's US plans are Early at $27 a month, Growing at $59 and Established at $97, with no per-user fees. Early allows quotes and 20 invoices a month and 5 bills; Growing and Established list no invoice cap. Xero is running 90% off for the first 6 months for new US customers until November 2, 2026; the discount does not apply to payment fees.

Online invoice payments run through Stripe. Xero's US fee page lists 2.9% + 30¢ for domestic cards, ACH debit at 1% capped at $9 per transaction, and bank transfer at 0.5% capped at $5.

What to watch:

• Early's 20-invoice cap. Ten invoices fit, but a business that sends more needs Growing.
• Payment fees are separate from the subscription and the promotion. Payroll is extra too; see payroll for small business.

Choose it if you want accounting software that the whole team and your accountant can use without paying per seat.

Square: best if you also take payments in person

Square's invoicing is included in every Square plan, including Square Free. The difference between plans is the processing fee:

Plus adds payment schedules (milestone payments on one invoice), custom invoice templates and batch invoices. Charging a saved card on file costs 3.5% + 15¢ on every plan.

What to watch:

• The Free plan's card rate is 3.3% + 30¢, the highest card rate here.
• Plus pays for itself only with large ACH invoices or the in-person and marketing features that come with it.

Choose it if you already use Square at a counter or on site (see what POS systems charge per in-person payment), and want invoices, in-person payments and payouts in one account. If you book appointments, salon software compares Square Appointments with booking tools on card fees.

PayPal: best when clients want to pay with PayPal

PayPal charges no monthly fee for invoicing; you pay per payment received. Its US invoicing rates are 2.99% + $0.49 for cards, Apple Pay and other wallets, 3.49% + $0.49 when the client pays with a PayPal account or Venmo, and 1% capped at $10 for ACH bank payments. Pay Later options cost 4.99% + $0.49, and invoices paid from abroad carry an extra 1.50%. PayPal also lists an optional Invoice Subscription Service at $14.99 a month.

What to watch:

• Clients paying through their PayPal balance cost you more (3.49%) than clients paying by card.
• The $0.49 fixed fee is higher than the usual 30¢.

Choose it if your clients already pay with PayPal or Venmo, or you invoice large amounts by ACH and want the $10 cap without a subscription.

Stripe Invoicing: lowest ACH cost on large invoices

Stripe Invoicing has no monthly fee. It charges 0.4% per paid invoice on Starter (0.5% on Plus, which adds quotes), on top of Stripe's payment fees: 2.9% + 30¢ for US cards and 0.8% capped at $5 for ACH Direct Debit.

On a $5,000 ACH invoice that is $5 plus the $20 Invoicing fee. On a $500 card invoice it is $14.80 plus $2.

What to watch:

• The Invoicing fee is on every paid invoice, on top of the payment fee: $40 on $10,000 a month at 0.4%.
• No accounting. Stripe records the payments, but you still keep your books in another tool.

Choose it if you have a developer, or already use Stripe, and invoice large amounts that clients pay by bank transfer.

How to choose

1. Want to spend nothing on software? Wave Starter if you also want bookkeeping (more free plans in free accounting software for small business); Zoho Invoice if you send under 500 invoices a year and want to pick your gateway.
2. Bill clients for time? FreshBooks, on the plan that matches your client count. Law firms that need trust accounting or LEDES invoices should see legal billing software instead.
3. Already on QuickBooks or Xero? Use their invoicing; the payment fees are close to everyone else's.
4. Take payments in person too? Square, on the Free plan unless large ACH invoices or its other features justify Plus.
5. Large invoices paid by bank transfer? Look for a cap: Stripe ($5), Xero's Stripe ACH ($9), PayPal or Square Plus ($10).
6. Whatever you pick, ask big clients to pay by ACH. On a $1,000 invoice that is $10 or less instead of about $30 by card.