Bookkeeper for Web Development Agencies

Keep project deposits, milestone payments, and recurring retainer revenue organized, so your books stay current, and you always know what you've earned and where your cash is going.

A web developer working on a client project at a large monitor with code visibly on the screen.

Quick Answers

The Two Questions Every Web Development Agency Asks Us First

What does bookkeeping cost for a web development agency?

We quote a flat monthly fee that starts at $300 a month. It doesn't change with the number of transactions, it changes with how complicated your business is to set up and run, like how many projects you bill, how many contractors you pay, and whether hosting and retainer income are part of the mix. We set your rate after a quick look at your books.

How should web development agencies track deposits and milestone payments?

Money comes in three ways: project deposits, milestone billing, and monthly hosting fees. The deposit goes onto the books as deferred revenue, and it becomes revenue when you bill the milestone. That keeps profit matched to the project. Developer and subcontractor costs land on the same project, and hosting income gets its own line so you can see the recurring side of the business.

Challenges

Where Web Development Bookkeeping Slows Down

Our Services

Our Services for Web Development Agencies

We keep the books for web development agencies, which means tracking project revenue, deposits, milestone payments, and retainers across months with very different cash flow.

Client Results

What Our Clients Say

  • They caught up our books quickly! , I was trying to figure out if I should hire an assistant to help free the business. They walked me through everything, honestly such a helpful call. Left feeling like I actually knew what to do next.
    Wade MarcyJune 2026
  • Incredibly responsive team. They got back to me almost immediately and had everything knocked out in a day. The whole experience was smooth and efficient. Would definitely recommend to anyone looking for quick, reliable service.
    Michael WrightJune 2026
  • Recently, we were introduced to Matt for bookkeeping services, and our experience has been excellent. Matt has been highly responsive, engaged, prompt in his communication, and consistently professional in his approach. We’ve appreciated his attention to detail and willingness to assist, and we would not hesitate to recommend his bookkeeping services to others.
    Michael TurgeonJune 2026

Why Equipped

Why Equipped

We've been in the room when cash is tight and a project is behind. That shapes the way we do bookkeeping for developers.

  • You Won't Have to Chase Us for an Answer

    When you have a question, you hear back the same business day. If you're in the middle of a project and need a number, you don't wait for tomorrow to decide what to do next.

  • Financials That Help You Run the Business

    We structure your reports so you can see which projects are profitable, what your monthly retainer is worth, and how much cash is actually available. That makes it easier to price new work, hire a contractor, or plan for a slow quarter.

  • Books You Can Rely On

    Every account is reconciled, each transaction is checked, and the founder reviews your books before they're delivered. You won't be second guessing whether your numbers are right when you're presenting them to a lender or looking for a better day to take a payout.

  • Bookkeeping Built Around What Owners Actually Need

    Our team ran a small business earlier than we did bookkeeping, so we know what it's like to wait on a payment and wear every hat. That's why we prioritize speed and honesty over inflated process, and why the numbers you get for hard decisions are ready.

Next step

Get a Quote on Your Bookkeeping

Tell us where your books stand and whether your income comes through projects, retainers, or both. We'll review the situation and give you a clear quote before anything begins.

In-Depth Guide

What Good Bookkeeping Looks Like for a Web Development Business

Most of the money in a web development business shows up in big payments, and then it waits in the bank while the work is still ahead. These pages explain what month to month bookkeeping for a business like yours actually looks like, and why a clean set of books is the tool you use to decide what to bid on and how to staff.

How does money actually flow through a web development business?

Most money comes in as project fees paid in stages: a deposit before the work starts, a milestone payment partway through, and a final invoice when the site is delivered. A smaller, steadier stream comes from clients who pay monthly for hosting and maintenance.

The timing is the whole point. The deposit and the milestone land in your bank account while the work is still in front of you. Your books need to hold that money as received but not yet earned, then move it into revenue as the work actually gets done. One accounting firm's page written directly for this trade says it plainly: web design and development agencies have accounting complexity around project cash timing, because deposits and milestone payments arrive as income when they are received, not when the work is complete. We could not find a better one-line description of your books anywhere. (https://www.coreaccountinggroup.com/web-designers)

The exact size of each payment differs from project to project. Some shops take a donation up front, others carry a long build on a small one. What does not vary is the order of events: the money arrives before the work is finished, and that timing gap drives most of what bookkeeping has to keep straight.

  • Project fees. A deposit, a milestone payment, and the final balance when the client accepts the site.
  • Recurring income. Hosting, care plans, and monthly retainers that bill the same amount every month.
  • Pass-through costs. Domains or hosting you buy for the client and resell at cost; the money comes in and goes out again, so it is not really your income.

What are the real costs of a web development business?

The biggest cost is people, which means subcontractors and your own hours. The tools, the hosting, and the domains are real but cheap by comparison.

Web developers report that selling can soak up at least half of their productive working hours. That time is actual cost of the whole pipeline, but it appears on no invoice and in no bank feed. So a book built only from bank statements will show a project making money while your own unpaid hours quietly eat the real margin. (https://www.reddit.com/r/webdev/comments/1pkbbzv/)

Subcontractors show up correctly when each invoice is tagged to the project it belongs to, and that makes per job profit a real number rather than a guess. A developer who hands you one total for all subcontractor work gives you a cost with a single line, and you have no idea which client it belongs to.

The fixed side is small. One web designer who published their own spending lists hosting at about $36 a month and a domain renewal near $13 for the year. Cost guides in the industry put domains at $10 to $50 a year and hosting from about $2 up to more than $100 where a dedicated server is paying for. Those add up to a few hundred dollars a month for tools you run on, which is real money but not the line that decides whether the business is profitable. (https://localcreative.co/blog/web-design-expenses/, https://www.iubenda.com/en/blog/website-development-cost/)

What usually goes wrong with web development books?

Two mistakes show up in more web development accounts than anything else, and both come from the same project shape. The first is not booking the deposit as income in the month it lands, and the second is mixing one off project revenue with recurring hosting in a single line.

When a deposit is recorded as income right away, a long build looks highly profitable at the start and like a money drain at the end. It is the same project from two wrong angles. The cash arrived on time, so the books call it profit before the work exists.

When hosting and recurring retainers share one line with project builds, the steady part disappears. It gets covered by big project invoices during busy months and you don't notice when a client cancels their hosting until the whole revenue number dips. The monthly member and the money you could count on, is hidden inside the lumpy project totals.

The third thing that goes wrong is owner hours. They never show up in the ledger at all, so the books quietly overstate how profitable the business is. If you spent three weeks of your own time making sure the next client had a project, that cost is in no invoice and no expense line.

What should you track separately?

The biggest point of division is revenue. Project income and recurring income belong in separate lines, and pass-through costs stay out of your revenue entirely. Get that split right and the rest falls into place behind it.

  • Project revenue, which is the one-off build income.
  • Recurring revenue, which is hosting, care plans, and all the retainers.
  • Pass-through costs, which are domains and hosting you buy for the client and bill back at cost. These sit outside the revenue lines because you never actually keep that money.

On the cost side, attach every subcontractor invoice to the project it belongs to, so the final project number is genuine: the total collected from the client, minus the subcontractor, minus outside costs and any pass-through you dropped in. That is the number you bid the next similar project on.

It is also worth being strict about the difference between the tools you pay for and the services the client pays for. A server you keep for client hosting is part of your cost. A monthly domain fee that bill goes through as pass-through, not as an extra line of your profitability.

Which reports and numbers matter most?

The numbers that matter most for a web business are per job, the split between project and recurring income, and your actual cash position. The total revenue for the year is not any of them.

Gross profit per job is the one you price the next bid on. It is the total fee minus the direct costs, the subcontractor and any outside. Without a history of per job numbers, every new quote is a guess about what last ones left.

The split between recurring and project income tells you what a typical month looks like. The recurring income larger, the more of your fixed cost is already covered before you begin the month, rather than waiting on a deposit that has not arrived.

Cash position is where the year's profit stops being useful. You could have a profitable year on paper and still be tight because a large project's balance hasn't appeared yet. The only way to see that coming is to look at the month ahead in cash and not in revenue.

LineGross marginNet margin
Computer Services25.52%4.40%
Business & Consumer Services33.50%5.45%
Advertising28.11%0.89%
Whole industry gross and net margins for the nearest service categories to a web development agency. There is no web development issue in an official table, so the close lines are the useful frame. Data is NYU Stern, presented by Vena. (https://www.venasolutions.com/blog/average-profit-margin-by-industry)

That table is a frame, not a target. It covers whole sectors, not your, but it tells you the shape: the kind of service work you do runs at about 25 to 33 cents of per dollar and ends with about 5 cents net margin. If your own ledger shows something far outside that, the problem is usually direct costs being hidden or income booked the moment it arrives.

How do you plan when the money comes in big chunks?

When most of your income lands in big lumpy project payments, you plan in cash, not revenue. The year's profit is real, but that does not tell you when the bills can be paid.

The practical view is two things: what is in the bank now, and which milestones are contracted but not billed. The first covers the business until the next deposit, but the second tells you how far out the deposit lands. One page with three or four lines for the next months is enough to see whether you can take the next hire or need to run an earlier invoice. It doesn't take extravagance, but it requires the book to see those two numbers at a glance, not in an annual report.

That is why the recurring hosting line matters so much in a project shop. It might be a small part of your income to make the quarter quiet, but it is the part that comes on schedule. It is the revenue that covers the base cost, and the projects become profit on a stable foundation.

Keep the books monthly rather than only at tax time. The pipeline deadlines schedule themselves around the milestone dates, and the month starts with cash position visible instead of a fuzzy pre-tax number that shows up at the end of the year.

Related reading: for the ongoing work that keeps the books current, try the full monthly bookkeeping service; if the records fell months and years behind, the catch-up bookkeeping service; for the report the off-the-shelf numbers hide, the custom financial reporting service. For the same trade on the page, also see web design agencies and software development companies. (https://equipped.com/services/monthly-bookkeeping, https://equipped.com/services/catch-up-bookkeeping, https://equipped.com/services/custom-financial-reporting, https://equipped.com/industries/web-design-agencies, https://equipped.com/industries/software-development-companies)

How It Works

How Starting Works, Step by Step

Your First Month

We review the deposits and milestone payments on projects, how they show up in the books, and the retainer and hosting income and what you pay subcontractors.

Review the business and current books

You get a clear look at the books without cleaning anything up first, and nothing gets changed before you have heard how we found it.

Who reviews your books

The Person Accountable for Your Books

Matt Cavanaugh
Your books are not handed off to an anonymous team with no clear owner. Matt oversees the quality of the bookkeeping and reviews the financial reporting before it reaches you.

Matt Cavanaugh

Founder, Equipped Bookkeeping

FAQ

The Questions Owners Actually Ask Us

Ask Your Question ›

Monthly bookkeeping starts at $300 a month, and the price is flat, so you are not paying by the hour or surprised. The exact number depends on how busy the business is and how complicated the books, but you get a clear price before we start.

Yes. Being behind is common, and a busy project season is usually why. We catch up the missing months first, fix anything that got recorded wrong, and then keep everything current going forward.

Yes. Most of our clients are owner run businesses, from a single person doing the work and the books to a small team with a few subcontractors. If you run it and you bill projects, you are exactly the business we work with.

Yes. We handle the monthly bookkeeping and your CPA keeps the tax side. We keep the books organized and reconciled so your CPA gets a complete and accurate set of books come tax time.

We do not run payroll or prepare taxes. We handle the bookkeeping side of both, like recording what gets paid out for staff or subcontractors, and we get everything ready so your payroll provider and CPA can do their part.

Very little. We have access to pull the bank and card transactions automatically, and we can see what the feed brings in. Usually we just need a quick note when something does not show up in the feed: a deposit that is not there, or a cost that went through without a bank record.

Deposits and milestone payments get recorded on the day they arrive, so the books match what actually came in. They stay tied to the project until the milestone is done, so a big deposit does not make your reports say the job is more complete than it is while you still have weeks of work on it.

Yes. We can set up the books so retainers, hosting, and one off project fees each show on their own line, since you see the reliable month over month income separately from the work that lands in chunks. That is where the real financial picture of an agency is in this trade.

That is where a lot of businesses start. We go through what is recorded inline, pull out what is real, and set up a proper set of books. The starting place does not matter, just a starting point.

Ready to Get Your Books Off Your Plate?

Tell us where your books stand and what you need help with. We'll take a look, tell you what we recommend, and give you a clear flat-rate quote before anything starts.