The best payment tracking software of 2026

FreshBooks is the tool we would hand a freelancer or small agency owner who loses track of who still owes them money. Every plan sends late payment reminders, adds late fees, sets up recurring invoices and lets clients pay online by card, digital wallet or ACH bank transfer.

The catch is the client limit. Lite costs $23 a month and covers only five billable clients. Plus costs $43 a month for 50 clients, and Premium costs $70 a month with no client limit. Select is priced on request and lowers card and ACH fees. New monthly subscribers currently get 80% off for four months, yearly billing takes another 10% off, and there is a 30-day trial with no card. Card payments cost 2.9% plus $0.30 and ACH payments cost 1% (prices checked November 4, 2026).

Choose it if you bill a modest number of clients for your time or projects and want reminders and late fees to run without you.

Skip it if you invoice dozens of small customers, because the jump from five to 50 clients pushes you onto Plus quickly, and Zoho Invoice or Wave cost less.

Zoho Invoice is free, and it covers what most small businesses need to track payments. You can send up to 500 invoices a year, set up recurring invoices and let automatic reminders chase late payers. Customers get a self-service portal where they can see and pay their invoices, and you can offer several payment options through connected gateways.

The free account allows two users, three projects and two organizations, which suits a sole trader or a two-person business. Invoices carry "Powered by Zoho Invoice" branding. Zoho points businesses that outgrow it to Zoho Billing, its paid product for subscriptions and more complex billing (checked November 4, 2026).

Choose it if you send fewer than about 40 invoices a month and want reminders and a client portal without a monthly fee.

Skip it if you need more than two users, unbranded invoices or accounting reports, where QuickBooks Online or Wave Pro fit better.

QuickBooks Online makes sense when payment tracking is one part of a wider job: you want invoices and your accounting in the same software, and an accountant who already knows it.

There is now a Free plan for one user that sends two invoices a month, or unlimited invoices if you qualify for and turn on QuickBooks Payments. From Simple Start up, customers can pay by card or bank transfer inside the invoice, and you get status updates and reminders. Simple Start costs $38 a month for one user, Essentials $85 for three users, Plus $140 for five and Advanced $340 for 25. The pricing page shows 50% off for three months and a 30-day free trial, without saying whether you can have both (prices checked November 4, 2026).

Choose it if you need proper accounts as well as payment tracking, or your accountant asks for QuickBooks.

Skip it if all you need is to send invoices and chase late payers, because FreshBooks, Wave or Zoho Invoice do that for less.

Wave's free Starter plan gives you unlimited invoices, estimates and bills, plus bookkeeping records and a cash flow dashboard. Wave notifies you when a customer views an invoice, when it falls due and when it is paid, and customers can pay by card, bank payment or Apple Pay once you switch on online payments.

Pro costs $19 a month or $190 a year. It sends overdue reminders on its own, 3, 7 and 14 days after the due date, imports and sorts bank transactions, captures receipts and lowers card fees. Recurring invoices with automatic card payments need Pro or online payments. Card payments cost 2.9% plus $0.60 on Starter, with Amex at 3.4% plus $0.60. On Pro the first 10 card payments each month drop the $0.60, then the standard fee applies again. Bank payments cost 1%. Wave lists prices in US and Canadian dollars (checked November 4, 2026).

Choose it if you are in the US or Canada and want unlimited invoices for free, with the option to add automatic reminders for $19 a month.

Skip it if you work outside the US and Canada, or take many small card payments, where the $0.60 fee on each one adds up.

Pabbly Subscription Billing, sold until recently as Pabbly Subscriptions, is for businesses that charge customers again and again, such as memberships, software and coaching programs. You create products and plans, share a checkout page and Pabbly records every one-time and recurring payment, sends branded invoices and keeps each customer's history in one place.

Its strongest point is gateway choice. It supports more than 35 payment gateways, including Stripe, PayPal, Square and Razorpay, in about 55 currencies, and you can show several on one checkout page. When a payment fails, Pabbly retries it, sends dunning emails on your schedule and can switch the customer to a different gateway at checkout. Customers can update or cancel subscriptions in a self-service portal, and there is a built-in affiliate module on the top plan.

The Free plan covers 50 customers with limited revenue and no team members. Standard costs $19 a month, or $17 a month billed yearly at $204, for 1,000 customers. Unlimited costs $79 a month, or $69 a month billed yearly at $828, and adds unlimited customers and the affiliate module. Pabbly charges no transaction fees of its own and offers a 30-day refund (prices checked November 4, 2026).

Choose it if you sell subscriptions through more than one gateway, or through Indian gateways such as Razorpay, Instamojo or Cashfree.

Skip it if you invoice clients for one-off projects, where FreshBooks or Zoho Invoice fit better.

Rebilly combines subscription billing, invoicing and payment orchestration, so you can connect more than one gateway account and decide where each charge goes. It also sells reporting and automation tools, though the pricing page does not say which plan includes which reports.

Basic costs $15 a month plus 1% of revenue, with one gateway account, no per-transaction fee and $0.05 for each 3D Secure check. Pro costs $125 a month plus 1% of revenue with volume discounts of up to 50% off that fee, and connects up to 10 gateway accounts, with the full rules engine for workflow automations and integrations. Enterprise is priced on request. Both public plans have a 30-day trial with no card (prices checked November 4, 2026).

The 1% fee adds up. At $20,000 a month in revenue you would pay $200 in revenue fees plus the plan, on top of your gateway's own charges.

Choose it if you run several merchant accounts and want one place to route, retry and track payments.

Skip it if you have a single Stripe or PayPal account, where Pabbly Subscription Billing charges no revenue fee.

PayWhirl adds subscriptions and payment plans to an existing store or website. It works as a Shopify app, with BigCommerce or on any website, and it charges through Stripe, Square, Braintree, Authorize.Net or PayPal. Customers manage their own subscriptions in a portal, failed payments are retried, and reports cover MRR, subscriptions, churn and customers.

You pay a monthly fee plus a percentage of each transaction, on top of your gateway's fees. For any website, Starter is free with a 3% fee, Business Pro costs $49 a month with 2%, Business Plus $149 with 1% and the top business plan $249 with 0.5%, all with a 14-day trial. The Shopify app has its own plans: free with 3%, Pro at $9 a month with 2%, Traction at $29 with 1.5% and Scale at $149 with 0.75% (prices checked November 4, 2026).

Choose it if you sell physical subscription boxes or payment plans through Shopify or BigCommerce and want customers to manage their own renewals.

Skip it if you sell services by invoice, because PayWhirl is built around checkouts and recurring charges.