Financial Clarity for Shopify, Automated by Bookkeep.

Whether you run multiple locations, franchise stores, or sell across channels, Bookkeep automates your revenue recognition, deposit reconciliation and sales tax compliance with 100% accuracy.

Trusted by top ecommerce and retail Shopify brands

Powerful automation for Shopify finance teams

Revenue Accounting Automation

Bookkeep syncs your sales data from Shopify and other channels like Amazon and PayPal directly to your accounting system with clean, daily accrual-based journal summaries. Properly recognize revenue at fulfillment and reconcile your deposits automatically.

Shopify
Amazon
Toast
Paypal
Square
Stripe
Quickbooks
Sage Intacct
NetSuite
Xero
Zoho Books

Sales Tax Compliance

Bookkeep automates sales tax from start to finish. We file and remit across all 50 U.S. states for you. Stay compliant as you scale, backed by our dedicated sales tax specialists.

Automatically Filed
Automatically Paid
Audit-Proof

Payout Splitting, Transfers & Reconciliation

Automatically split Shopify payouts by store, franchisee, or sales channel. Bookkeep transfers funds to the right bank accounts and reconciles every deposit in your GL.

Deposit Transfers
Gift Card Transfers
Buy Online, pickup in-store transfers

Support your merchants with smarter financial workflows

If you’re a Shopify agency or implementation partner, Bookkeep helps your merchants automate their sales data, deposits, and tax — and saves you time during onboarding and ongoing support.

Partner with Us

Work at Shopify? Help your merchants automate their accounting

If you're on Shopify's sales, success, or partnerships team, Bookkeep is the financial automation platform your merchants have been asking for. We automate journal entries, sales tax, and payout reconciliation — so your merchants stay happy and scale faster.

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Integrations

Connect Bookkeep with your entire tech stack.

Shopify, Amazon, Toast, Square, PayPal, Stripe, QuickBooks, Xero, NetSuite, Sage Intacct
See all Integrations

You're not just getting software. You're getting a team.

Bookkeep is built and supported by experienced accountants, controllers, and automation pros. Whether you're running one Shopify store or 50, we’ve seen it — and solved it.
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What Shopify merchants are saying

See how Bookkeep provides financial clarity for leading Shopify brands.
Read Case Studies
Logo shop sante
“With Bookkeep, we finally found a reliable and efficient solution to connect Shopify and QuickBooks. Managing the accounting for our franchise network is now streamlined and secure. Today, we have the peace of mind that every transaction is perfectly reconciled and that every cent is properly distributed to our franchisees. Bookkeep has become an essential partner for Shop Santé, and we highly recommend their services to any business looking for accurate and efficient accounting automation.”
eric fortier
Eric Fortier
Founder
Logo shop sante
“The closing process has gotten so much more simple because of Bookkeep. We now have real-time numbers that I’m confident are right, giving us the ability to do a lot more higher-level analysis, which is better decision-making for the business.”
eric fortier
Brian Thalman
Financial Controller
Logo shop sante
“I now can take a breath and focus on streamlining procedures, think about the culture I want my company to have, and focus on clients that are better matched for my process… I am now more focused on HR, marketing, and growth. I spend more time on my own company’s financials, which I NEVER did… I also meet with peers, partners, and potential clients in meetings throughout the day, in addition to webinars that I like to participate in.”
eric fortier
Rachel Dauchy
Owner
Logo shop sante
“One of the things I really love about Bookkeep is its compliance area. I can find everything quickly and can see exactly how the entries are calculated and booked, since it’s linked to platforms like Square or Shopify. I have no worries if there is ever an audit… No one else does this. Bookkeep works so well, I forget I’m using it!”
eric fortier
Sherri-Lee Mathers
CPB, AIA
Logo shop sante
“I would just simply recommend Bookkeep because of the confidence that it gives when your transactions are posted and it tells me to expect a payment and then the payment comes in that, that boosts my confidence. I’ve never been able to reconcile the clearing accounts and I would like to be able to do that and we’re closer now than we’ve ever been.”
eric fortier
Forrest Allen
Head of Accounting
Logo shop sante
“All of my e-commerce clients are now on Bookkeep. Bookkeep allows me to provide transparent reports that match the sales platforms on a daily basis. It allows me the opportunity to move forward at a better speed, growing my business efficiently.”
eric fortier
Maureen Stevens
Founder
Logo shop sante
“Bookkeep has saved me hours of time dealing with our clients accepting payments from Square, Shopify, Amazon, etc. This application allows us to even grab historical data as we are wrapping up client books for tax prep. The support is superior. This is a must have tool for every accounting professional.”
eric fortier
Dawn Brolin
CPA, CFE, Owner
Logo shop sante
“My time is worth something. The free time Bookkeep is giving me is more than worth it. By saving a lot of hours each month with Bookkeep, I can work on important things. It’s an investment, not an expense.”
eric fortier
Chip Adkins
Chef/Owner