Financial clarity for Shopify franchise operations
Bookkeep automates accounting for every corporate store and franchisee — with clean journal entries, payout splitting, royalty collection, and built-in sales tax compliance across your entire network.
Trusted by top ecommerce and retail Shopify brands
Franchise-ready accounting automation, from HQ to each store
Automated journal entries by franchisee
Post daily, accrual-based summaries for each franchise location — without manual uploads.
Separate entries for each franchise store or ecommerce channel
Consistent chart of accounts across the network
Compatible with QBO, Xero, NetSuite, Sage Intacct
Consolidated & franchise-level financial reporting
Keep each franchisee’s books clean while maintaining HQ oversight.
Individual P&Ls and balance sheets per franchisee
Consolidated group reporting for corporate entities
Works with any franchise accounting structure
Payout splitting & royalty transfers
Automatically split Shopify payouts and send the right funds to the right accounts.
Collect royalties and franchise fees from franchisees
Allocate gift card redemptions back to issuing locations
Transfer BOPIS sales revenue to the pickup store
Payout reconciliation by location
Reconcile every payout across corporate and franchise accounts.
Match Shopify deposits to your accounting system by store
Spot and fix discrepancies automatically
Support for multi-bank and multi-entity setups
Integrated sales tax support
Track and file sales tax accurately for each franchise location.
Map tax settings per store or POS
File at the local, state, or consolidated level
No spreadsheets or manual mapping required
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.
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.
Multi-bank settlement for Shopify
Automated reconciliation — from franchisee deposits to HQ transfers
Bookkeep reconciles every Shopify payout, splitting funds by store or franchisee and matching deposits to your accounting system. Whether it’s a shared POS, a BOPIS sale, or a gift card redemption between stores, Bookkeep ensures every dollar is accounted for and audit-ready.
What Shopify merchants are saying
See how Bookkeep provides financial clarity for leading Shopify brands.
“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
Founder
“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.”
Brian Thalman
Financial Controller
“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.”
Rachel Dauchy
Owner
“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!”
Sherri-Lee Mathers
CPB, AIA
“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.”
Forrest Allen
Head of Accounting
“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.”
Maureen Stevens
Founder
“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.”
Dawn Brolin
CPA, CFE, Owner
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“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.”
Chip Adkins
Chef/Owner