1099 contractor accounting · September 20, 2026
Best accounting software for 1099 contractors (2026)
Income, expenses, and a file that survives January. Paying 1099s out is contractor payments — a sibling page. Classification is counsel.
By Gregory GreensteinUpdated September 20, 2026Affiliate disclosure
1099 contractor accounting fails when every platform payout and every gas receipt lives in a personal account and January is a 1099-NEC surprise. The job is: a business-named account, a ledger you will open, and invoices if you bill. This page is for people who receive 1099s — independents, not the company issuing twenty of them (that is contractor payments plus a payroll product).
Wave is the $0 default. FreshBooks wins when invoices are the product. QuickBooks Online wins when the CPA already lives there. Xero wins when the bookkeeper already lives there. We will not tell you that you are correctly classified. That is counsel.
Side-hustle bookkeeping and freelancer accounting are siblings. Contractor invoicing is the trades bill. This page is the file for a US 1099 independent.
Prices as of September 21, 2026. This is not tax advice on quarterly estimates or reasonable compensation if you later elect S-corp. We are not your accountant.
The short list
Public list prices as of September 20, 2026. Promos change. Confirm on the vendor page before you buy.
| # | Product | Best for | Public starting price | Score |
|---|---|---|---|---|
| 1 | Wave | 1099 independents who will reconcile a bank feed and send a few invoices | Accounting and invoicing $0. Wave Pro $19/month or $190/year. Confirm waveapps.com/pricing. | 8.5 |
| 2 | FreshBooks | 1099s who live on invoices, time, and late reminders | Lite $23/mo for 5 billable clients; Plus $43 for 50; Premium $70. Team $11/person. | 8.3 |
| 3 | QuickBooks Online | 1099s whose CPA already speaks QuickBooks — or who will elect S-corp | Simple Start $38/mo; Essentials $85; Plus $140; Advanced $340. | 8.1 |
| 4 | Xero | 1099s whose bookkeeper already lives in Xero | US published: Early $25, Growing $55, Established $90. US list step announced $27 / $59 / $97 from October 1, 2026. Confirm xero.com/us/pricing-plans. | 8.0 |
01
Wave
1099 independents who will reconcile a bank feed and send a few invoices
Public pricing: Accounting and invoicing $0. Wave Pro $19/month or $190/year. Confirm waveapps.com/pricing.
Wave official pricing, reviewed September 21, 2026.
Skip if
A CPA already asked for QBO, or you will not open the file. Software you ignore is a shoebox.
Why it ranks
- A real $0 ledger. That is the first-year 1099 job.
- Invoices without a $38 habit.
- A path you can hand to a CPA if you keep it clean.
- See Is Wave worth it and when to leave spreadsheets.
Watch-outs
- You still have to categorize.
- Quarterly estimates are not a Wave toggle.
- Pro is easy to ignore and keep paying.
- Not payroll. If you hire W-2s, see first-hire payroll.
02
FreshBooks
1099s who live on invoices, time, and late reminders
Public pricing: Lite $23/mo for 5 billable clients; Plus $43 for 50; Premium $70. Team $11/person.
FreshBooks US pricing, reviewed September 21, 2026.
Skip if
You only needed a $0 feed. Wave is enough. Or the CPA is QBO-only.
Why it ranks
- AR and time match how many 1099s actually get paid.
- Lite is honest at five clients. Plus is the usual roster.
- See Is FreshBooks worth it and freelancer invoicing setup.
- Useful when Wave’s reminders are the leak.
Watch-outs
- Lite’s five-client cap.
- Still not a deep inventory ledger.
- Your CPA may still want QBO at year-end.
- Retainers: see the consultant retainers page if that is the leak.
03
QuickBooks Online
1099s whose CPA already speaks QuickBooks — or who will elect S-corp
Public pricing: Simple Start $38/mo; Essentials $85; Plus $140; Advanced $340.
Intuit public pricing, reviewed September 21, 2026.
Skip if
You send a handful of invoices and will not open the file weekly. Start with Wave.
Why it ranks
- The US CPA network is the product the week this stops being a side 1099.
- Simple Start is enough for many sole props who invoice and reconcile.
- Same family as Workforce if you later hire. We still prefer Gusto for most first W-2s.
- See how much QBO costs and Is QBO worth it.
Watch-outs
- You still have to categorize.
- List prices stepped in 2026.
- Do not buy Plus for a single 1099.
- Desktop is a different article.
04
Xero
1099s whose bookkeeper already lives in Xero
Public pricing: US published: Early $25, Growing $55, Established $90. US list step announced $27 / $59 / $97 from October 1, 2026. Confirm xero.com/us/pricing-plans.
Xero US pricing plans, reviewed September 21, 2026.
Skip if
Your CPA only opens QBO. Do not buy Xero to look international.
Why it ranks
- Unlimited users on published plans — you plus a bookkeeper without a seat tax.
- Bank rec is why people stay.
- Pairs with Gusto if you hire.
- See Is Xero worth it.
Watch-outs
- US payroll is not Workforce.
- October 2026 US list step is real.
- If every local CPA is QBO-only, you bought a conversion.
- Not FreshBooks. AR-first shops should compare honestly.
How we picked
The job is a US 1099 income file: bank feed, invoices, a CPA-ready close. We scored $0 honesty and advisor adjacency. Issuing 1099s to others is contractor payments. AI tax bots stay on Aiacent.
Who should skip this page
- Companies paying a roster of 1099s — contractor payments plus payroll.
- W-2 employees tracking expenses — gig expenses if you are actually 1099; otherwise your employer’s T&E.
- Trades invoicing jobs — contractor invoicing.
- Anyone mixing payouts with rent and hoping software unmixes it.