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Agencies juggle retainers, project work, contractors, and pass-through costs like ad spend. We keep it all clean and show you profit by client and project, so you know exactly which work is worth it.
Clean books are the difference between running your agencies business on real numbers and running it on guesswork. We give you accurate, up to date bookkeeping and clear reporting, so every decision, from pricing to hiring to your next investment, rests on what is really happening in your business, not a rough estimate at year end.
Why it is different
An agency can be fully booked and barely profitable if project costs and contractor time are not tracked against the right clients. Retainers, deferred revenue, and pass-through costs like ad spend make it easy to misread your margins.
We track profit by client and project, handle retainers and deferred revenue correctly, separate pass-through costs, and keep contractor payments clean, so you can see which clients actually make you money.
What we handle
Costs tracked to clients and projects so profit is clear.
Retainer revenue tracked and recognized correctly.
Freelancer and contractor payments organized.
Ad spend and pass-through costs separated from your revenue.
Client invoicing kept on schedule.
Clear profit by client and project.
Proven on Upwork
Since 2021, HOLO Bookkeeper has completed work for more than 1500 clients on Upwork and Fiverr, earning Top Rated status. Here is the kind of feedback agencies clients leave, and you can read the full portfolio and reviews yourself.
Set up profit tracking by client and finally showed us which accounts were dragging us down.
Agency Owner · USA · Upwork ClientClean monthly books and clear reporting for our marketing agency. Highly recommended.
Creative Director · USA · Upwork ClientSee the full Upwork portfolio and reviews → · Connect on LinkedIn →
How it works
Tell us about your business, your platforms, and where your books stand today.
We connect your accounts and tools with read only access wherever possible.
We build the right chart of accounts and catch up or clean up if needed.
Reconciled books and clear reports every month, plus automation where it helps.
Why choose HOLO Bookkeeper
You get the accuracy and dedicated attention of an in house bookkeeper, on demand, for only the work your agencies business needs, plus automation most in house hires never build.
QuickBooks ProAdvisor and Xero Certified Advisor with over 6 years and 1500+ clients.
You work with the person doing the work, with replies within 24 hours.
The same secure, certified process wherever your business is based.
We remove repetitive work with Excel, Sheets, and Python, so you pay for judgment.
Services and related industries
Related industries:
Free tools
Agency accounting guide
Agencies sell time and expertise, often through retainers, projects and pass-through media spend. The P&L can look healthy while a few clients quietly consume most of the team’s hours. Agency bookkeeping should answer one question every month: which clients and services actually make money?
A retainer billed in advance is earned as the work is delivered. On accrual books, prepaid retainers sit in deferred revenue and are recognized over the period they cover. Project fees billed in milestones follow the same logic.
When you buy ads or media on a client’s behalf and re-bill them, record the cost and re-billing consistently so gross revenue isn’t inflated and your true agency fee income stays visible. Many agencies report “net revenue” (fees minus pass-through costs) as their key number.
Tag revenue and direct costs (staff time, freelancers, software) by client or service line using classes in QuickBooks or tracking categories in Xero. Paired with time tracking, this shows effective hourly rates by client. Try the free profit margin calculator on a single retainer.
Collect W-9s up front and file Form 1099-NEC for contractors paid above the threshold ($2,000 for payments made in 2026 and later, $600 before). Classify people correctly. See 1099 vs W-2.
Agencies often pay staff before clients pay invoices. An AR aging review each week keeps collections on track. Use the free AR aging tool.
General information as of 2026, not tax advice. Confirm sales tax and income tax treatment with your tax preparer.
Questions and answers
Yes. We track costs against clients and projects so you can see which work is actually profitable.
Yes. Retainer revenue is tracked and recognized correctly over the service period.
Yes. Pass-through costs are separated so they do not distort your real revenue and margin.
Yes. Freelancer and contractor payments are tracked and kept organized.
QuickBooks or Xero, plus automation and dashboards where useful.
Usually within a few days. After a short consultation we scope the work, agree a clear price, and begin, starting with catch-up or cleanup first if your books need it.
Yes. We work with agencies in all 50 states, fully remotely, with the same secure and certified process everywhere.
Retainers billed in advance are recorded as deferred revenue and recognized as income over the period the work covers.
Track pass-through media costs and the matching client re-billing in dedicated accounts, so you can report net revenue (your fees) separately from money that simply passes through.
Tag revenue and direct costs by client with classes or tracking categories, and combine that with time tracking to compare effective hourly rates across clients.
Book a free 15 minute consultation and we will set up agency books that show real client profit.
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