Best Expense Management Software for Agencies with Project Billing

Agencies lose margin when expenses, time tracking, and client billing live in separate tools. The right setup ties project costs to budgets, billable flags, and invoices — so nothing slips into overhead. But here's the nuance most roundups gloss over: the platforms that do that tracking are delivery tools. They manage the workflow of time, expense, and budget. What they don't fully handle is the money-movement layer — collecting payment, reconciling across currencies, paying contractors, and getting cash into your account.

That's where the picks below come in. Think of this as a two-stack decision: choose a PSA or expense-tracking platform for the operational core, then bolt on a payments layer that handles the actual money. The four products here cover the latter — invoicing and payment collection, multi-currency accounts, client-facing checkout, and the legal and banking foundation for agencies just starting out.

What the category leaders do (and don't)

The expense management category is well-covered by dedicated platforms. Productive is the all-in-one choice for professional services and agencies, connecting costs directly to client work, budgets, approvals, and profitability.1 BigTime is built for firms that need time, costs, billing, invoicing, and project work in the same system.1 Harvest excels at visual project budget tracking.3 Expensify leads on receipt-scanning automation.3 TMetric, FreshBooks, QuickBooks Online, and Bonsai round out the agency billing field, with most platforms landing between $12 and $15 per user per month. Business plans across the broader time-and-expense category average $10 to $25 per user per month.

These tools handle the tracking and billing workflow — time entries, expense logs with receipts, billable versus non-billable flags, approval chains, and invoice generation.3 But when it comes to actually moving money — collecting from clients in multiple currencies, paying international contractors, or setting up the banking infrastructure a new agency needs — they typically integrate with external payment processors rather than handling it natively. Stripe and PayPal integrations are explicitly called out as common additions for online payment collection.2

In other words: you still need a payments layer. Here are the things actually worth buying.

1. Stripe Invoicing — the payment-collection layer

If your PSA tool generates the invoice, Stripe Invoicing collects the money. It's a global invoicing platform built to deliver invoices faster, speed payment, and handle tax calculations and currency conversions.4 For agencies, that means automated invoices that clients can pay via card or bank transfer, multi-currency support, and reconciliation that feeds back into your project billing — all at a low per-invoice cost.

The case for Stripe as the top pick is simple: it's one of the two payment processors most commonly integrated into agency billing tools,2 and it handles the part of the workflow where money actually changes hands. Your expense platform tracks the cost; Stripe collects it.

2. Wise Business — multi-currency accounts for international agencies

Agencies with international clients and remote contractors face a problem most billing tools don't solve: currency conversion eats margin. Wise Business gives you a multi-currency account with low FX fees, so you can bill in a client's currency, pay contractors in theirs, and reconcile project expenses across borders without losing a slice to exchange-rate markups.

This sits alongside your expense platform rather than replacing it. Your PSA tool tracks what's billable; Wise handles the cross-border money movement that follows.

3. PayPal for Business — client checkout flexibility

Not every client wants to pay by card or bank transfer. PayPal for Business offers a trusted, globally recognised checkout and invoicing option — useful for agencies billing clients who prefer PayPal's payment flow. It complements a dedicated expense or PSA platform by giving clients one more way to pay, which means fewer delayed invoices and less time chasing.

PayPal is already one of the two payment integrations most commonly built into agency billing software,2 so adding it as a client-facing option is usually a low-friction extension of what your stack already supports.

4. Stripe Atlas — formation and banking for early-stage agencies

Before you can manage expenses, you need a legal entity and a bank account. Stripe Atlas bundles company formation, banking setup, and tax configuration into a single process — relevant for agencies in their first year that need to establish the billing foundation before layering on expense management software.

This is a setup-stage pick. Once your entity exists and your bank account is open, the expense-tracking and payments tools above become the operational stack. Atlas is how you get there.

How to choose

Start with your delivery platform. If you're an agency that bills clients for time and expenses, pick a PSA or expense tool first — Productive for all-in-one agency operations,1 BigTime for deep professional-services billing,1 Harvest for visual budget tracking,3 or Expensify for receipt automation.3 Most of these run $10 to $25 per user per month.2

Then add the payments layer. Stripe Invoicing for collecting on project bills. Wise Business if you work across currencies. PayPal for Business for clients who prefer it. Stripe Atlas if you haven't formed the company yet.

The two-stack approach isn't a workaround — it's how agency billing actually works. The tracking tools track; the payments tools pay. Getting both right is what keeps margin from leaking into overhead.

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