FreshBooks Alternatives for Agencies (2026)

If your agency is outgrowing FreshBooks because of client caps or the $11 a month per team member, LotsInvoice is a direct swap for the invoicing part: $12 a month per business with unlimited clients, invoices and team members, and no cut of payments. If you want $0, use Zoho Invoice or Wave. If you need full accounting, QuickBooks Online or Xero.

I opened every vendor's own pricing page on 19 October 2026 and judged each one on what an agency actually pays for: the monthly price, what each teammate adds, how many clients or invoices the plan allows, whether accounting is included, and what is taken from each payment. Prices are US dollars before tax, monthly unless noted. Sources are linked at the end.

Why agencies look for a FreshBooks alternative

FreshBooks is good software. It's accounting with strong invoicing: expenses, time tracking, double-entry reports, bank reconciliation, card and ACH payments built into the invoice, proposals and client retainers on Plus, and a mobile app. If you want all of that in one place, it's a solid choice.

The friction for agencies comes from how it's priced:

• Client caps. Lite lets you invoice 5 billable clients, Plus 50, and Premium is unlimited. FreshBooks counts both active and archived clients toward the limit.
• Team members cost extra. Every plan adds $11 a month per team member. Select, the custom plan, includes 2.
• Card fees on every payment. FreshBooks Payments, and Stripe connected to FreshBooks, charge 2.9% + $0.30 per card payment and 1% for ACH.

A four-person agency on Plus, with the owner and three teammates, pays $43 plus 3 × $11, so $76 a month at list price. FreshBooks also offers a 30-day free trial.

FreshBooks alternatives for agencies at a glance

Checked on 19 October 2026 on each vendor's own pricing page.

1. LotsInvoice: invoicing only, with the whole team included

An invoice is your name on a request for money. It should be right. I built LotsInvoice for agencies, freelancers and small businesses who invoice their own clients and don't want an accounting suite to do it.

• One price per business, the team included. Starter is $12 a month or $120 a year for one business (from $10 a month billed yearly). Pro is $29 for 5 businesses and Business is $79 for 20, for groups that run several brands or sister companies. Inside a business, clients, invoices, estimates, credit notes, items, templates, reminders and team members are unlimited. Your project manager and your bookkeeper join as editors or viewers, and the price doesn't change. Pro and Business include LotsNotes Pro. See pricing.
• No client caps. The 51st client costs the same as the first: nothing extra.
• Set up once. Your logo, colours and font, one of nine designs (US Letter or A4) or your own template, your numbering, your columns, item and accounting codes, custom fields, tax IDs and declarations. If a client wants a PO number on the page, that's a setting.
• Nothing goes out unchecked. Every invoice starts as a draft next to a preview of the real PDF. Totals, discounts and several taxes per line are calculated to the cent and match in the preview, the PDF and the reports. You send it when you are ready.
• A record you can trust. Sent invoices are numbered and locked. Changes are revisions with a reason, or credit notes.
• Followed up until you're paid. The invoice goes from your business name with the PDF and a private client portal link, and replies come to you. You see when it's opened. Reminders go out before and after the due date, in your words, and stop when it's paid.
• Retainers and quotes. Recurring invoices weekly, monthly or yearly, as drafts to review or sent on schedule. Estimates accepted with a typed name, converted in one click. Any currency.
• Never holds your money. Your invoices show the payment options you already use: a Stripe Payment Link, PayPal, Square, bank transfer, ACH, Zelle, Venmo or check. Clients pay you directly, your provider's own fees apply, and LotsInvoice takes nothing. You record the payment when it arrives.
• Reports for your accountant. Who owes what, revenue, tax collected and payments, with CSV export, and a full export of your data whenever you want.

New accounts get 15,000 free credits, valid 90 days, no card, enough to run one business for a month.

Where FreshBooks still fits better: LotsInvoice doesn't do bookkeeping, bank feeds, time tracking or expenses, and it doesn't process cards inside the invoice or mark invoices paid automatically. If you want those in the same app, keep reading. Start at lotsinvoice.com.

2. Zoho Invoice: free, if two users are enough

Zoho Invoice costs $0, forever. It covers quotes, recurring invoices, automated payment reminders, customizable templates, a self-service customer portal, expenses, time logging with projects, and reports, and it connects to Zoho CRM, Books and Analytics. You can run up to two organizations under one account, and there are mobile apps.

The limits are on its pricing page: up to 2 users, a maximum of 3 projects, up to 500 invoices a year, and "Powered by Zoho Invoice" branding.

Choose Zoho Invoice if your agency is two people, you send fewer than 500 invoices a year, and Zoho's branding on your invoices is fine.

3. Wave: free invoicing with bookkeeping

Wave's Starter plan is $0 and includes unlimited estimates, invoices, bills and bookkeeping records, plus a mobile app. Card payments cost 2.9% + $0.60 (3.4% + $0.60 for Amex). Pro is $19 a month or $190 a year and adds bank imports, receipt capture, automated late-payment reminders and users with admin, editor or viewer roles. On Pro, the first 10 card payments each month cost 2.9% + $0. Pro is priced per business, so three businesses on Pro are three subscriptions.

Choose Wave if you want invoicing and simple bookkeeping in one place and you're happy to take card payments through Wave. It's the closest free match to what FreshBooks does.

4. Invoice Ninja: low-cost Pro with unlimited clients

Invoice Ninja's Free plan gives you unlimited invoicing for up to 5 clients, 11 templates, your logo, recurring invoices, a client portal, project time tracking and expenses. Ninja Pro is $14 a month or $140 a year and adds unlimited clients, custom designs, automatic late-payment reminders, P&L reports, a REST API and up to 10 companies under one login, without Invoice Ninja branding.

Adding account users starts on Enterprise, priced by the number of users: $18 a month for 1 to 2 users, up to $300 a month for 51 to 100, with per-user permissions and bank account sync. There are apps for desktop and phone, and you can self-host it.

Choose Invoice Ninja if you're a small team that wants a full-featured invoicing tool at a low monthly price, or you want to host it yourself.

5. QuickBooks Online: full accounting, priced by users

QuickBooks Online is a full accounting suite, priced by the number of users. Simple Start is $38 a month for 1 user, Essentials $85 for 3, Plus $140 for 5 and Advanced $340 for 25. There's a 30-day free trial, and the pricing page also links to a $0 QuickBooks Free plan. QuickBooks Payments charges 2.99% for cards and 1% for ACH.

Choose QuickBooks Online if your accountant works in QuickBooks and you want invoices, bookkeeping and payments in one system.

6. Xero: accounting with a low entry price

Xero's Early plan is $27 a month and lets you send quotes and 20 invoices. Growing is $59 and Established is $97; Established adds multiple currencies and project time and cost tracking. Online invoice payments carry fees set by Xero.

Choose Xero if you want full accounting and your agency bills in several currencies (Established), or your accountant prefers it.

7. Harvest: invoice from tracked hours

If your agency bills by the hour, Harvest starts from the timesheet. Free is 1 seat and 2 projects with time tracking, invoicing and expenses. Teams is $11 a seat a month ($9 billed annually) with unlimited seats, team reporting, and accounting and payment integrations such as QuickBooks Online, Xero and Stripe. Enterprise is $17.50 a seat ($14 annually). On paid plans, Harvest says extra invoices, projects, clients and tasks are billed based on what you use. There's a 30-day trial.

Choose Harvest if tracked time is the source of truth for what you bill.

8. Bonsai: proposals, contracts and invoices per user

Bonsai is a client and project suite for freelancers, agencies and consultancies, priced per user. Invoices and payments start on Essentials at $25 a user a month ($19 billed annually), together with proposals, contracts, scheduling and a client portal. Premium ($39, or $29 annually) removes Bonsai branding and adds QuickBooks and Xero integrations. Elite ($59, or $49 annually) has a 3-user minimum. There's a 7-day trial.

Bonsai Payments charges 2.9% + $0.30 for cards and 1% for ACH ($1 minimum). Its help center says that where Bonsai Payments is available, getting paid through Stripe or PayPal instead adds a 1% platform fee.

Choose Bonsai if you sell with proposals and contracts and want them in the same workspace as your invoices.

9. HoneyBook: client flow for service businesses

HoneyBook runs the client journey from lead forms to proposals, contracts, invoices and payments, with a client portal and unlimited clients and projects on every plan. Billed yearly, Starter is $29 a month, Essentials $49 and Premium $109. Essentials allows up to 2 team members and adds a QuickBooks Online integration and removal of HoneyBook branding; Premium has unlimited team members and multiple companies. Card payments start at 2.7% + $0.10, and ACH is 1.5%.

Choose HoneyBook if you book clients through proposals and contracts and want payment taken inside the same flow.

Which FreshBooks alternative should your agency pick?

• You want exact, on-brand invoices with the whole team included, and you don't need accounting in the same app: LotsInvoice, from $10 a month billed yearly.
• You want $0: Zoho Invoice (2 users, 500 invoices a year) or Wave Starter.
• You want accounting like FreshBooks: Wave Pro, QuickBooks Online or Xero.
• You want a low price with unlimited clients: Invoice Ninja Pro at $14.
• You bill hours: Harvest.
• You sell with proposals and contracts: Bonsai or HoneyBook.

How to move from FreshBooks to LotsInvoice

Keep FreshBooks open while your last invoices there get paid, and start new work in LotsInvoice:

1. Create your business with your legal name, address and email, then confirm the email from your inbox.
2. Set it up once: logo, design, columns, taxes and payment options (your Stripe Payment Link, PayPal, bank or Zelle details).
3. Bring your clients and services as CSV files: customers (up to 1,000 rows at a time) and items.
4. Continue your numbering. Set the next invoice number so INV-0148 follows INV-0147, with no gap your accountant has to explain.
5. Invite your team as editors or viewers.
6. Send your first invoice from a draft, after checking the PDF preview.

LotsInvoice also works with the AI agent you already use, when you want it. If you work in Claude or ChatGPT, connect it at lotsinvoice.com/mcp and give it the setup in one message:

Read https://lotsinvoice.com/skill.md. Then set up my agency in LotsInvoice: import the clients in clients.csv and the services in services.csv, continue invoice numbering from INV-0148, and add my Stripe Payment Link and bank details as payment options. Draft the first invoice for Acme and show me the preview before anything is sent.

It asks before anything goes out, and the dashboard is where you check everything.

FAQ

What is the best FreshBooks alternative for agencies?

It depends on what you use FreshBooks for. If it's invoicing and you want your whole team included at one price, LotsInvoice charges per business with unlimited clients and team members. If you need accounting, QuickBooks Online, Xero or Wave. If you bill tracked hours, Harvest. If you sell with proposals, Bonsai or HoneyBook.

Is there a free alternative to FreshBooks?

Yes. Zoho Invoice is free for up to 2 users and 500 invoices a year, with Zoho branding. Wave Starter is free, with bookkeeping, and charges 2.9% + $0.60 per card payment. Invoice Ninja is free for up to 5 clients. LotsInvoice has no free plan; new accounts get 15,000 free credits, valid 90 days, no card.

How much does FreshBooks charge for team members?

$11 a month per team member on Lite, Plus and Premium. The custom Select plan includes 2 team members. Checked on FreshBooks' pricing page on 19 October 2026.

Does FreshBooks limit the number of clients?

Yes, by plan. Lite lets you invoice 5 billable clients, Plus 50 and Premium unlimited, and FreshBooks counts both active and archived clients toward the limit. LotsInvoice has no client limit inside a business.

Can I keep taking card payments if I leave FreshBooks?

Yes. With LotsInvoice, add your own Stripe Payment Link, PayPal or Square link and it appears on every invoice and in the client portal, next to bank, ACH or Zelle details. Clients pay you directly, your provider's fees apply, and you record the payment when it arrives.

Sources

All checked on 19 October 2026:

• FreshBooks: freshbooks.com/pricing
• LotsInvoice: lotsinvoice.com, pricing, skill.md
• Zoho Invoice: zoho.com/us/invoice/pricing
• Wave: waveapps.com/pricing
• Invoice Ninja: invoiceninja.com/pricing-plans
• QuickBooks Online: quickbooks.intuit.com/pricing, payment rates
• Xero: xero.com/us/pricing-plans
• Harvest: getharvest.com/pricing
• Bonsai: hellobonsai.com/pricing, help center: payment methods and fees
• HoneyBook: honeybook.com/pricing