Best Invoicing Software for Web Design Agencies Compared

On this page 7 sections

1. What Invoicing Software for a Web Design Agency Must Handle
2. Stripe Invoicing: Fees and Flexibility
3. QuickBooks Online Payments: Accounting-First Billing
4. HoneyBook vs. Bonsai vs. Dubsado: Proposal-to-Payment Tools
5. Fee Comparison on a $10,000 Project Invoice
6. Choosing an Agency Invoicing Tool by Team Size and Billing Model
7. Next Steps

Key takeaways

• Agencies need deposits, milestone schedules, recurring retainers, and low-cost ACH. Many generic invoicing apps handle only some of these well.
• On a five-figure project, the payment method affects your fees more than the software does. A capped or flat ACH fee can cost a small fraction of a percentage-based card fee.
• Check whether a tool charges for invoicing on top of card processing. Add any monthly subscription to your per-invoice math, and remember that fixed fees and caps repeat with each milestone.
• Match the tool to your team size and billing model. Solo designers usually want proposal-to-payment simplicity. Growing agencies usually want accounting integration and control over processing costs.

Choosing invoicing software for a web design agency takes more than finding a clean invoice template. Agency billing usually starts with a deposit, moves through two or three milestone payments, and then becomes a monthly maintenance or hosting retainer that can run for years. If a project stops partway through, see our guide to web design kill fees and getting paid when a client cancels mid-project. If a project grows beyond its original scope, see our guide to web design change orders and billing scope creep. This guide compares Stripe Invoicing, QuickBooks Online, HoneyBook, Bonsai, and Dubsado on the features agencies actually use. It also shows how processing fees add up on a single large project invoice, so you can estimate what each setup costs before you commit.

A note on pricing: Processing rates, invoicing add-on fees, ACH caps, and subscription tiers change often and vary by plan. This article describes how each tool charges instead of quoting rates. Confirm current pricing on each provider's site before you decide. All numbers below are illustrative.

What Invoicing Software for a Web Design Agency Must Handle

Generic invoicing apps are built for one-off bills: you finish the work, send an invoice, and get paid. Agency billing works differently, and these are the gaps that usually cause problems:

• Deposits before work starts. You want the deposit paid before you schedule discovery, ideally on the same page as the contract signature.
• Milestone schedules. A common structure ties payments to design approval, development completion, and launch. The tool should generate and send each installment automatically so you don't have to track them yourself. For help structuring the terms, see our guide to web design deposit and milestone payment terms.
• Recurring retainers. Maintenance plans, hosting, and SEO retainers need automatic card or bank charges, retries for failed payments, and support for card updaters. Our article on automating monthly retainer billing for maintenance plans covers the setup.
• ACH bank payments. Business clients paying five-figure invoices often prefer bank transfer, and ACH usually costs you far less than cards.
• Fee handling on big invoices. You may want to keep a card option while recovering part of the cost through surcharging or dual pricing where permitted.
• Clean accounting sync. Each partial payment needs to post to the right client and project in your books.

Before you compare tools, write down your billing model: project-only, project plus retainer, or mostly retainer. That one decision narrows the field quickly.

Stripe Invoicing: Fees and Flexibility

Stripe Invoicing runs on top of Stripe's payment platform, and its main strength is flexibility. You can send hosted invoices that accept cards and bank payments. If you or a developer on your team are willing, you can automate nearly anything through the API. Recurring billing for retainers runs through Stripe's subscription tools.

How Stripe Charges

Stripe's cost on an invoice can have two layers:

1. Payment processing. Cards carry a per-transaction fee, and ACH bank debits have a separate fee structure. Check whether ACH is capped per transaction on your account.
2. The invoicing layer. Depending on your plan, Stripe may charge a fee for invoicing on top of processing or include it in a subscription tier. Check the current terms, because even a small add-on percentage adds up on large invoices.

Where It Fits Agencies

• It suits technical teams that want custom deposit and milestone automation.
• Its ACH option is worth steering clients toward on large invoices.
• Large or unusual payments can trigger reviews or holds on aggregator-style accounts. If that happens, our guide to why Stripe may hold a big web design payment explains the common reasons.

If you're still choosing a core processor, our comparison of Stripe, PayPal, and Square for web designers goes deeper on account structure. If you're applying for a dedicated account, see why processors flag web design agencies and how to get approved.

QuickBooks Online Payments: Accounting-First Billing

QuickBooks Online is accounting software first, and its invoicing and payments are built around your books. That is the main reason agencies choose it. Paid invoices reconcile automatically, and partial payments post to the right customer without manual entry.

How QuickBooks Charges

• You pay a monthly QuickBooks Online subscription, and features vary by tier.
• Processing fees for cards and ACH are charged separately through QuickBooks Payments. The card rate may differ depending on whether the client pays through an online invoice or you key in the card.
• Progress invoicing and deposit handling may depend on your plan, so confirm your tier includes what you need.

Stripe Invoicing vs. QuickBooks: The Short Version

Agencies can also keep QuickBooks as the system of record and process payments through a separate merchant account. MannyPay supports a QuickBooks integration for merchants who want their books in QuickBooks and their processing handled elsewhere.

HoneyBook vs. Bonsai vs. Dubsado: Proposal-to-Payment Tools

These three are client-management platforms, sometimes described as CRMs for creative businesses. Invoicing is one step in a longer workflow that starts with an inquiry form and ends with a paid final invoice. For many solo designers and small studios, that bundling is the main appeal.

Feature sets and plan limits change, so confirm current capabilities before you move your client list.

Questions to Ask Before Choosing One

• Does the payment schedule send milestone invoices automatically, or do you trigger each one yourself?
• Can clients pay by ACH, and how is ACH priced compared with cards?
• Can you add a card fee or offer a cash-price discount, and does the tool let you do that compliantly in your state?
• Which processor runs underneath, and can you choose it?
• How does the tool export to your accounting software?

Fee Comparison on a $10,000 Project Invoice

This comparison is where the decision becomes concrete. The table uses illustrative pricing structures, not any specific vendor's rates. It shows how the structure of a fee drives your cost on a large invoice. Plug in each provider's current published rates to run your own version.

What the Illustration Shows

• The payment method matters more than the software. In this example, a percentage card fee costs about $290 more than a capped ACH fee on one invoice.
• Add-on fees compound. An invoicing fee on top of processing applies to every milestone.
• Milestones change some costs and leave others alone. Uncapped percentage fees cost about the same whether you bill once or in milestones. Fixed per-transaction fees and per-transaction caps, such as capped ACH, apply to each installment, so a three-part schedule can multiply those costs. In the illustrative capped ACH row, a 50/25/25 split costs about $30 ($10 × 3) instead of $10 for a single payment. That's still far below the card cost, but it's worth factoring in when you set your schedule.
• Subscriptions are part of the cost. Divide a tool's monthly fee by the number of invoices you send each month to get a true per-invoice figure.
• Business and commercial cards often cost more to accept than consumer cards under interchange-based pricing, and clients paying agency invoices often use them.

To see what a reasonable rate looks like for your volume, read what web design agencies should pay in card fees. If you bill clients abroad, see our guide to getting paid by international web design clients.

Recovering Card Costs on Large Invoices

Many agencies keep cards as an option and pass part of the cost to the client. The two common compliant approaches are credit card surcharging where permitted and dual pricing that shows cash and card prices. Rules vary by state and by card network, and disclosure requirements apply. Our guide to passing card fees to clients on large web design invoices covers the details. Confirm your obligations with a qualified professional before you add fees.

Choosing an Agency Invoicing Tool by Team Size and Billing Model

Solo Designers: What a Freelance Web Designer Invoicing App Should Do

In a one-person shop, time is the scarcest resource. Look for:

• One link that covers the proposal, contract, and deposit
• Automatic milestone reminders
• An easy ACH option for clients
• Simple recurring billing for a handful of maintenance clients

HoneyBook, Bonsai, or Dubsado often fit here, as long as the subscription cost makes sense for your invoice volume.

Small Studios (Two to Ten People)

At this size, reconciliation starts to take real hours. Consider:

• QuickBooks Online as the system of record, with or without a separate processor
• A proposal tool for sales that syncs to your accounting
• Whether flat-rate card pricing still makes sense as your monthly volume grows

Growing and Retainer-Heavy Agencies

When recurring revenue makes up a large share of your income, processing costs and payment stability matter more than templates. If you resell hosting, see our guide to reselling hosting to clients, including billing, markups, and failed payments. Focus on:

• A dedicated merchant account with transparent pricing
• Recurring billing with retries and card-updater support. Our guide on how to choose recurring billing software can help.
• A virtual terminal for keying in large client payments when a client calls in a card
• Documented scope and approvals, which help if a client disputes a charge after launch. See winning web design chargebacks after a site launches.

Next Steps

1. Map your billing model: deposit, milestones, retainers, and the payment methods your clients prefer.
2. Pull your last three months of statements and calculate your real per-invoice cost, including subscriptions and add-on fees.
3. Shortlist two tools that handle your workflow. Then compare their current processing and invoicing fees using the table above, and count how many installments each project will have.
4. Decide whether to steer large invoices toward ACH, recover card costs compliantly, or both.

If you'd like a second look at your processing costs, MannyPay offers payment processing for web design agencies, including merchant accounts, virtual terminals, and cost programs such as surcharging and dual pricing where permitted. You can request a free processing quote, and a MannyPay specialist will respond within one business day.

ME

About the author

MannyPay Editorial Team

Beyond the Swipe's editorial desk researches the publication's guides and news and cites its sources in every article. Articles reviewed by a named MannyPay editor carry that editor's byline.

This article is for general educational purposes and is not legal, tax or financial advice. Card network rules and state laws change; confirm current requirements for your business.