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.

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
My Bookkeeper Doesn't Respond to Me
You need an answer about a client's deposit or a project costing, and the bookkeeper gets back to you for days. The books may technically be getting done, but you can't rely on the person handling them when you need a response now.Read The Breakdown ›I'm Way Behind on My Bookkeeping
Weeks go by with launches, client deadlines, and the books sit. When they finally get pulled together, the invoices and hosting charges are out of order, and you have to rebuild half the month from memory over a weekend.Read The Breakdown ›Revenue Is Up, But I Still Don't Feel More Profitable
More websites are going out the door, but the costs that come with them, design tools, contractor labor, software subscriptions, and card fees, keep climbing. The bank account doesn't feel like it goes with the workload, and the books don't show why.Read The Breakdown ›I Don't Know What a Project Actually Made
You take a deposit, pay a freelancer for the build, and bill the final payment at launch months later. The cash lands in one month, but the expenses are spread across all of them, so a project that looks like a huge win on the books can still look like a loss.Read The Breakdown ›I Can't Tell if Recurring Work Makes Money
Hosting and maintenance renewals come in every month, but that's not true. The books don't separate this stream from its own costs, so you can't tell whether the retainer matches the work.Read The Breakdown ›I Don't Know if I Can Afford Another Hire
You want to bring on a developer or do real sales work, but the books don't give you a clean answer. One busy month of project revenue can fund it, and the next quiet one can drain it. A lumpy P&L doesn't show what a steady salary actually costs.Read The Breakdown ›
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.
Monthly Bookkeeping for Web Development Agencies
For agencies that want a reliable month to month bookkeeping. Each project's deposits, milestone payments, and retainer income are tracked and reconciled, and expenses like subcontractors, hosting, and software are properly classified. That means the books stay current and you can see what each project is really earning. You get clear numbers for pricing, hiring, and planning ahead.
Explore Monthly Bookkeeping ›Catch-Up Bookkeeping for Web Development Agencies
For agencies that have fallen behind on the books. We go through the past, rebuild the income schedule for each project, reconcile every account, and sort out any payments that were never recorded. You get a complete and current set of books and a clean start to move forward, without the backlog.
Explore Catch-Up ›Clean-Up Bookkeeping for Web Development Agencies
For agencies whose existing books don't match what's actually happening. We sort through the old transactions, split one-time project fees from recurring retainers, and fix where income was posted before the work was done. Expenses like developer costs and contractor fees are put in the right places. The result is books you can trust and depend on.
Explore Cleanup ›
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 2026Incredibly 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 2026Recently, 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.
| Line | Gross margin | Net margin |
|---|---|---|
| Computer Services | 25.52% | 4.40% |
| Business & Consumer Services | 33.50% | 5.45% |
| Advertising | 28.11% | 0.89% |
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.
A straight summary of what is working, what is not, and a flat price to fix it before any work begins.
Explain the findings and give a flat quote
What we find is a clear explanation of the situation.
The starting point fits your books, whether that means catching up, cleaning up, or moving straight into the monthly routine.
Get the books into the right starting condition
Messy books are not a barrier. We start from wherever things are.
A dependable close each month, with the reports reviewed and questions answered the same day.
Take over the monthly bookkeeping
Month end becomes predictable, not a scramble, and you always know where you stand.
Who reviews your books
The Person Accountable for Your Books

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
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.
