Automated Accounting for Multi-Location Shopify Retailers
Financial clarity for multi-location Shopify retailers
Bookkeep automates accounting for every store and franchisee — with clean journal entries, payout splitting, deposit transfers, and built-in sales tax compliance across your entire operation.
Trusted by top ecommerce and retail Shopify brands
Location-level clarity, franchise-ready control
Automated, Store-Level Accounting
Post daily, accrual-based summaries from each POS or ecommerce store.
Separate entries for each store, POS, or ecommerce entity
Consistent mappings across locations
Compatible with QBO, Xero, NetSuite, Sage Intacct
Multi-entity financial reporting
Keep every store, region, or franchisee cleanly separated in your books.
Individual P&Ls and balance sheets
Group-level and consolidated views
Works with any accounting entity structure
Payout splitting & inter-company transfers
Automate Shopify payout allocation and bank transfers across stores and entities.
Transfer BOPIS funds to pickup location
Allocate gift card redemptions back to issuing store
Collect royalties or franchise fees from franchisees
Payout reconciliation
Reconcile every deposit, refund, fee, and tax by location.
Match Shopify payouts to your bank by store
Spot and fix discrepancies automatically
Support for multi-account and franchise banking setups
Integrated sales tax support
Track and file sales tax accurately across jurisdictions.
Map tax settings by store or POS
File at the local, state, or consolidated level
No need for spreadsheets or manual mapping
How payout splitting and deposit automation work
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Bookkeep can breakout your Shopify payout by POS location, as well as, automatically transfer funds to the appropriate bank account net of any fees, sales tax, chargebacks and other adjustments.
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See how Bookkeep supports multi-location and franchise structures — right from Shopify.
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
Split and transfer payouts by location, automatically
Bookkeep automates payout splitting across bank accounts by store, franchise, or fulfillment location—and transfers funds accordingly. Franchise fees? We collect those too.
Sales tax across all channels, filed for you
Bookkeep pulls Shopify’s tax data for each store, POS location, and jurisdiction — then calculates, maps, and files your taxes automatically, without manual work or reconciliation errors.
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
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
Sherri-Lee Mathers
CPB, AIA
Eric Fortier
Founder
Brian Thalman
Financial Controller
Rachel Dauchy
Owner
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
%201.avif)
“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
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner
Forrest Allen
Head of Accounting
Maureen Stevens
Founder
Dawn Brolin
CPA, CFE, Owner
%201.avif)
Chip Adkins
Chef/Owner