Creative & production services
Books and taxes for Shopify agencies.
A store build deposit, a Shopify Partner referral payout, a Plus migration that ran three months, and app subscriptions billed through your account. Gus sorts all of it, an accountant checks every transaction, and you get one number a month.
- From $197 a month
- An accountant on every transaction
- Cancel whenever
September came in at $19,100. The Callahan Leather Plus migration wrapped, so I moved that whole deposit out of prepaid work and into real income this month.
- Callahan Leather migrationMigration and build fees
- Shopify Partner payoutPartner referral income
- K. Yamamoto dev contractContract developers
- Klaviyo pass-through x6App costs billed to clients
- Postscript agency planSoftware
Why your books are different
Shopify agency books go wrong at the referral payout and the app bill.
A generalist sees deposits and a software bill. Your business is store build milestones, a Shopify Partner referral check, app subscriptions billed through your account on a client's behalf, and long Plus migrations that span months. When the books blend those, you cannot see what the agency is actually earning.
-
1
The Partner referral payout looks like ordinary sales
Shopify pays you a referral commission when a client you brought on stays subscribed, and that check can arrive months after the build wrapped, disconnected from any invoice you sent.
What we doBooks the referral payout as its own income line, separate from build fees, so you can see what recurring referrals actually add up to. -
2
App subscriptions billed to clients get counted as your expense
You set up Klaviyo or Postscript on a client's behalf and pay the bill so it is one invoice, then bill the client back. If only the outgoing charge gets recorded, it looks like your own overhead is climbing.
What we doBooks what you charge the client back as income and the app cost as an expense, so pass-through app costs do not distort your real overhead. -
3
A Plus migration spans months and one deposit
A Shopify Plus migration can run twelve weeks with a single deposit up front, so the month the deposit lands looks flush and the months of actual work look unpaid.
What we doHolds migration deposits until the matching milestone ships, so income lands with the work it paid for. -
4
A theme developer looks like a plain software cost
A contract developer brought in for custom Liquid theme work gets paid across a few invoices that can land in the same bucket as your monthly app subscriptions.
What we doTracks contract developer payments by name so labor cost per build and the 1099 total are both ready. -
5
Launch day support gets billed like routine maintenance
A client goes live on a big sale day and needs hands-on support that day, work that is really an add-on but often gets folded into a flat monthly retainer.
What we doFlags one-time launch support billed alongside a retainer so it counts as project income, not routine monthly work.
Your categories
The categories Gus keeps for a Shopify agency.
Set up once for how you get paid and what you spend. You never pick a category. He does, and an accountant checks it.
Money in
- Migration and build feesStore builds and Plus migrations, billed and counted as milestones ship.
- Partner referral incomeCommission payouts from Shopify for clients you referred.
- App costs billed to clientsWhat clients pay you back for apps you manage on their behalf.
- Maintenance retainersMonthly plans for ongoing store updates and support.
- Launch day support feesOne-time hands-on help billed apart from routine maintenance.
Money out
- Contract developersFreelancers brought in for Liquid theme work or custom app builds.
- App costs billed to clientsKlaviyo, Postscript, or similar apps run through your account on a client's behalf.
- SoftwareYour own agency tools and internal app subscriptions.
- Shopify Plus feesFees passed through for large client stores on the Plus tier.
- Stock assetsPhotos, icons, and fonts licensed for storefront builds.
- Payment processor feesWhat Stripe or PayPal kept before an invoice cleared.
What we watch for you
- Referral income
What Shopify pays you in commissions, tracked apart from build fees you invoice yourself.
- Migration backlog
Deposits collected on builds not yet delivered, so you know what is really yours to spend.
- Build margin
What a migration or build brought in against contractor cost, so you know which projects are worth it.
- The set-aside
What you will owe across migrations and referral income, tracked monthly so April holds no surprise.
Ask Gus
Things Shopify agency owners ask Gus.
Text him like you would text anybody. He answers in plain English, and when a question is above his pay grade, an accountant looks and gets back to you.
That is a Partner referral commission. I book it as its own income line, apart from your build fees, so you can see what it adds up to over the year.
I book both sides. What you pay the app is an expense and what she pays you back is income, so it does not look like your overhead is growing when it is really hers.
If he is not on payroll and you paid him $2,000 or more in 2026, he gets a 1099-NEC by January 31. I have been tracking his payments all year.
The tax side
The tax side of a Shopify agency.
Most of what goes wrong here is separating referral income and pass-through app costs from the agency's real earnings.
What your return has to get right
Your accountant signs it, so it gets done right the first time.
- Contractor 1099s for development helpAny developer not on payroll paid $2,000 or more in 2026 gets a 1099-NEC by January 31. Gus tracks every contract developer's total across migrations and builds.
- The pass-through deductionMost owner-operated Shopify agencies can take up to 20 percent of business profit off their taxable income when referral and build income is tracked cleanly all year.
- Equipment and software write-offsBusiness laptops, monitors, and annual software licenses can usually be written off the year they are bought, same as your Partner program tools.
- Self-employment tax for solo buildersA one-person agency pays 15.3 percent self-employment tax on top of income tax, so the set-aside has to cover both, separate from any pass-through app costs.
Deductions Shopify agencies miss
Your bookkeeper knows what to look for in your statements. You never have to.
- Contract developer fees
- Theme and app licenses
- Stock photos and icon sets
- Domain registrations
- Design and dev software
- Continuing education courses
- Partner program event costs
- Computer and monitor upgrades
- Coworking or home office share
- Payment processor fees
- Portfolio site hosting
- Client onboarding tools
General information about 2026 federal rules, not advice for your business. Your accountant looks at your actual numbers before anything gets filed.
All year, not just April
A Shopify agency year, kept every month.
Migrations and referral income both run on their own clocks. Your team keeps you ahead of the season and the return. Every month in between, your bookkeeper closes the books and speaks up the moment something looks off.
- January
New year, new builds
Last year's return gets started, the developer 1099 list is ready, and clients start planning migrations ahead of the next sales season.
- April
Filed. Done.
Your return is filed and signed while migration season is in full swing. No surprise bill, since the set-aside started back in January.
- July
Halfway check
Where you stand, what you will owe, and how Partner referral income has moved since January.
- October
Before the holiday rush
Clients push launch and support work before the big sales season, so Gus flags any equipment or software worth buying before December.
What you get
What you pay depends on what your business needs, and it does not move after that, busy season or slow. No hourly bills, no surprise invoices, no setup fee.
Book a call- Monthly bookkeeping
Every transaction sorted into categories set up for Shopify agencies. You never categorize a thing.
- An accountant checks every transaction
Real review, every month, before your books close. Not a spot check.
- Your business tax return, filed
Prepared, reviewed, and signed by that same accountant every year.
- The monthly number
What you made, what you spent, what to set aside for taxes.
- Your own bookkeeper
A real person assigned to your business, in the app whenever you need them. No hold music.
- On your books all year
Every month, not just in April. Your team speaks up whenever something is worth your attention.
- Cancel any time
No contract. No cancellation call. Your books are yours.
Straight answers
Questions Shopify agency owners ask first.
Do I need to connect my Shopify Partner dashboard to Gus?
No. Gus works from your bank and payment statements, so referral payouts and build fees get sorted without connecting to your Partner account.
I bill clients back for apps I run on their behalf. Does that count as my income?
Yes, the amount they pay you back is income and what you paid the app is an expense. Gus books both, so pass-through costs do not distort your real overhead.
A Plus migration took four months with one deposit up front. How does that get booked?
Gus holds the deposit until the milestone it was paid for actually ships, so income lands with the work, not the day the money moved.
My developer is paid through a mix of invoices and Venmo. Does that matter for the 1099?
No, Gus tracks the total paid to him across the year no matter which way the money moved, so the form is accurate either way.
My books have never been separated from my personal account. Can Gus still help?
Yes. Send what you have, even if it is a mess. Gus sorts it, the accountant checks it, and most owners know where they stand within a week.
Is a real accountant checking my books?
Yes. You get your own bookkeeper, Gus does the first pass on every transaction, and an accountant checks every one before your month closes. That same accountant prepares, signs, and files your business return. Goatkeeper is not a CPA firm, and we never pretend a person looked when they did not.
What does it cost, and can I cancel?
It starts at $197 a month, depending on what your business needs. No setup fee, no hourly bills, no contract. Cancel any time from the app, and your books go with you.
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What makes a bookkeeper worth paying for Every business we keep books for
Book a call
Pick a time. That's the whole signup.
Fifteen minutes with a real person on our team. They look at where your books are, tell you straight what it takes to get caught up, and get you set up on the spot if it fits.
- $197 a month to start
- An accountant on every transaction
- Cancel whenever