Best invoicing software for small businesses and freelancers
Last reviewed: September 2026
The best invoicing software depends on how clients pay. Most tools charge about 2.9% plus 25¢ to 60¢ per card payment and more on Amex. Simple charges 2.79% on every card with no per-invoice fee, from $99/mo for 5 users.
Competitor pricing last reviewed September 2026. Published rates change; check the vendor's current pricing page: FreshBooks pricing, QuickBooks pricing, HoneyBook pricing, Wave pricing, Bonsai pricing, Zoho Invoice pricing.
What does invoicing software charge per payment?
Subscription prices get the headlines, but card fees are the bigger bill once invoices get paid. This table lists what each tool takes when a client pays by card, by Amex and by bank, and what is locked behind a plan.
| Software | Price | Card on invoices | Amex / corporate | ACH | Notes |
|---|---|---|---|---|---|
| Simple | $99 / $199 / $399 (5 / 10 / unlimited users) | 2.79% | 2.79% | Accepted | No client limits |
| FreshBooks | Lite $23 (5 clients), Plus $43 (50 clients), Premium $70; +$11 per seat | 2.9% + 30¢ | 3.5% + 30¢ | 1%, uncapped | Proposals and retainers need Plus |
| QuickBooks Online + Payments | Simple Start $38 to Advanced $340 | 2.99% | 2.99% | 1%, $1 min; the old cap is no longer shown | Full accounting |
| HoneyBook | Starter $36, Essentials $59, Premium $129 | 2.9% + 25¢ | 3.4% + 9¢ per HoneyBook's blog; its pricing page says no premium card fees | 1.5% | Must use HoneyBook Payments |
| Wave | Starter free, Pro $19 | 2.9% + 60¢ | 3.4% + 60¢ | 1%, $1 min | Accounting included |
| Bonsai | Essentials $25/user, Premium $39/user | 2.9% + 30¢ | 3.25% + 30¢ | 1%, $1 min | 1% extra platform fee if you use Stripe or PayPal instead of Bonsai Payments |
| Zoho Invoice | Free (500 invoices/yr) | 2.9% + 30¢ | Not published | 0.8%, $5 cap |
Published by each vendor, reviewed September 2026. QuickBooks Payments fees shown are for invoice card payments. Simple accepts ACH on invoices.
Which invoicing software is cheapest for a freelancer?
Picture a solo designer billing $6,000 a month across 12 invoices of $500, all paid by Visa or Mastercard, with no Amex.
Simple Small: $6,000 x 2.79% = $167.40/mo + $99 = $3,197/yr
FreshBooks Lite: $6,000 x 2.9% + 12 x $0.30 = $177.60/mo + $23 = $2,407/yr (5 clients or fewer)
Wave Pro: $6,000 x 2.9% + 12 x $0.60 = $181.20/mo + $19 = $2,402/yr
What does a 5-person firm pay?
Now scale up to a 5-person firm invoicing $25,000 a month by card in 20 invoices, with 40% paid by Amex or corporate cards. The team logs billable hours, so it needs time tracking and invoicing software in the same app. On /pricing, time tracking tools sit in the Operations Hub on Medium, so Simple is priced at $199.
Simple Medium: $25,000 x 2.79% = $697.50/mo + $199 = $10,758/yr
HoneyBook Premium: $778.72/mo + $129 = $10,893/yr
FreshBooks Plus + 4 seats: $791/mo + $87 = $10,536/yr
Bonsai Essentials x 5: $766/mo + $125 = $10,692/yr
Dubsado Premier + 1 user: $731/mo + about $80 = about $9,732/yr
Here the totals bunch up. Simple is about $135 under HoneyBook and within about $220 of FreshBooks and Bonsai; Dubsado is about $1,026 cheaper. Without project time tracking, Simple Small comes to $9,558/yr. The fees on Amex are where per-payment pricing hurts the others most.
Does invoicing software need to do accounting?
Not always. QuickBooks, FreshBooks and Wave are accounting packages that also send invoices. Simple works the other way round: it is built around getting paid, with proposal software, estimates, retainers and reminders, plus expense tracking and a live P&L. It has no general ledger, bank reconciliation or tax filing.
If you need full bookkeeping, keep QuickBooks, FreshBooks or Wave. If you mostly need to bill clients and get paid faster, read about Simple invoicing or the wider consulting software setup.
Which invoicing tool fits which business?
- Simple is best for teams invoicing larger amounts by card, especially corporate cards.
- FreshBooks is best for solo service providers who want invoicing and accounting together.
- Wave is best for very small businesses that want free invoicing and accounting.
Detailed breakdowns: Simple vs FreshBooks and Simple vs HoneyBook.
Who should choose FreshBooks, Wave or QuickBooks instead?
- Solo freelancers with a few clients, where FreshBooks Lite or Wave Pro is cheaper per year.
- Businesses that want one tool for invoices and the books, since Simple is not accounting software.
- Businesses paid mostly by bank transfer with small card volume, where a capped ACH fee like Zoho Invoice's matters more than card rates.
Frequently asked questions
It depends on who pays and how. Solo freelancers with few clients usually pay least on FreshBooks Lite or Wave. Teams billing corporate clients by card tend to do better on Simple, which charges 2.79% on every card with no per-invoice fee.
QuickBooks publishes 2.99% for invoice card payments, Amex included, and 1% for ACH with a $1 minimum; the old ACH cap is no longer shown. That is on top of a QuickBooks Online plan from $38 to $340 a month.
Among the tools compared here, Simple's 2.79% with no per-invoice fee is the lowest card rate, and it applies to Amex too. QuickBooks charges 2.99%, and most others charge 2.9% plus 25¢ to 60¢.
Yes. Wave Starter and Zoho Invoice are free, with Zoho capped at 500 invoices a year. You still pay card fees: Wave charges 2.9% + 60¢ and Zoho 2.9% + 30¢ per card payment.
Yes. Simple logs billable hours by project, task or team member and generates invoices from tracked time. Time tracking tools are in the Operations Hub on the Medium plan at $199 a month for 10 users.
Get paid on every card for 2.79%
Invoices, retainers, reminders and payment links, with no per-invoice fee.