Ever look at your Shopify payout and wonder where your money went?
You’re not imagining things. Shopify tells you how much you’ve sold. But what lands in your bank account is almost always less. Between fees, refunds, timing differences, and sales tax, your numbers can feel more like a puzzle than a profit report.
If you’ve ever said “Our accounting is all over the place,” you’re in good company.
That’s exactly why Bookkeep exists.
Bookkeep is a powerful accounting automation platform that takes the complexity out of multi-channel, multi-entity financials. It pulls in your data from Shopify (and other sales channels), posts daily summaries to your books, and keeps your numbers clean, compliant, and easy to understand.
Let’s unpack how it works, and why it’s become the go-to tool for Shopify businesses, franchises, and growing retailers who need clarity, not chaos.
The Challenge: Why Shopify Accounting Gets a Little Messy
Let’s begin by saying that we LOVE Shopify! It is an incredible platform for modern commerce, and not only because it integrates your online store, POS, and other channels into one ecosystem. However, from an accounting perspective, that convenience often hides a headache.
Shopify reports your gross sales, but your payout is net of:
- Shopify and payment processor fees
- Refunds and chargebacks
- Sales tax collected
- Timing delays (sales today, payouts later)
- Multi-store or multi-bank settlements
So even if you’re using QuickBooks or Xero, you might still find yourself manually entering data, cross-checking numbers, and guessing which payouts belong to which sales.
The bigger your business grows, especially if you operate across multiple entities or locations, the more tangled this process becomes.
That’s where Bookkeep shines and why we love them!
The Solution: Bookkeep Automates Shopify Accounting Step-by-Step
Bookkeep turns messy, multi-channel accounting into a simple, automated workflow.
Here’s how it works:
1. Connect Your Sales Channels
Bookkeep connects with Shopify, Amazon, Square, Stripe, PayPal, and other sales platforms. It automatically syncs all your transactions. No manual exports or CSV uploads required.
2. Capture and Summarize Daily Data
Instead of pushing thousands of individual orders into your accounting system, Bookkeep summarizes your transactions into clean daily journal entries. That means you get:
- Accurate financials every single day
- Shorter reconciliation time
- Faster QuickBooks or Xero performance
3. Automate Revenue, Fees, and Deposits
Bookkeep creates and posts your sales journals and deposit journals automatically. It breaks out the revenue, fees, and payouts so everything balances beautifully, without you lifting a finger.
4. Reconcile Automatically
No more manual matching. Bookkeep ties your payout deposits back to the exact sales activity, making reconciliation nearly instant.
5. Get a Daily Summary Report
Every morning, you’ll get an easy-to-read email summarizing your day’s sales, deposits, and any exceptions that need your attention. You can spend minutes instead of hours reviewing your numbers, and skip the guesswork entirely.
Why Businesses Choose Bookkeep: Key Advantages
1. Multi-Bank Settlement (Game-Changer for Franchises)
If your Shopify setup deposits money into different bank accounts for different locations or entities, Bookkeep can handle that automatically. It knows how to route and record each store’s revenue correctly, a lifesaver for multi-store or multi-entity businesses. Bookkeep is the only company we know of that does this. Even Shopify doesn’t do this themselves.
Example: One of our Bookkeep clients, Angler’s All, runs three locations across two companies with separate bank accounts. Before Bookkeep, reconciling this setup was a nightmare. Now, their books automatically reflect the right data in the right accounts, and they only need to check in a few times a week instead of daily.
2. Summarized Journal Entries Save Time and Improve Accuracy
Unlike other tools that sync orders one-by-one, Bookkeep posts summarized entries for each day. This method keeps your financials clean and QuickBooks or Xero files lean. You get the detail you need without drowning in data. PLUS, you save up to 20 hours a month!
It’s the difference between “every single transaction” and “a clear picture of what really matters.”
3. Automated Sales Tax Compliance
Sales tax is complicated, especially across multiple states. Bookkeep takes that off your plate entirely. Their dedicated sales tax compliance team files and pays your taxes automatically.
Bookkeep already has established relationships with all 50 U.S. states, ensuring your filings are on time, accurate, and hassle-free. Our sister company TVP NYC uses Bookkeep for this very reason, the peace of mind and responsiveness make a world of difference.
4. Client-First Support and Communication
Bookkeep’s customer experience is one of its biggest strengths. Many accounting automation platforms stop at “set it and forget it,” but Bookkeep stays hands-on.
Their team is known for proactive communication, clarity, and responsiveness. They don’t just build smart tools, they build strong relationships.
Who Bookkeep Is Perfect For
Bookkeep was designed for multi-channel, multi-entity businesses that outgrew spreadsheets a long time ago.
It’s ideal for:
- Franchises with multiple locations or corporate/franchise setups
- Retailers selling both online and in physical stores
- Businesses with multiple QuickBooks files or bank accounts
- Growing eCommerce brands managing Shopify, Amazon, and POS systems simultaneously
In short: if your accounting is fragmented, Bookkeep helps you unify it.
Real Impact: Saving Time, Eliminating Guesswork
One client put it perfectly:
“Before Bookkeep, we were logging into our books every day to see what Shopify did. Now, we just review the daily summary email. It flags anything that needs attention, and most days, everything just balances.”
That’s the kind of automation that doesn’t just save time, it gives back your sanity.
Why Bookkeep Is Different from Other Accounting Integrations
Most accounting connectors push raw data. Bookkeep interprets your data.
It’s built by accountants who understand that sales, refunds, fees, and taxes need to land in the right accounts, on the right days, and in the right entities.
That’s why Bookkeep’s system is dynamic. It is able to adapt to complex organizational structures while most other vendors are linear and limited.
Final Thoughts: Bringing Clarity Back to Your Numbers
Bookkeep isn’t just an automation tool, it’s a clarity engine for your business finances.
It helps you:
- Automate accounting across multiple sales channels
- Simplify reconciliation
- Stay compliant with sales tax regulations
- Gain transparency into daily performance
Whether you’re managing one Shopify store or a multi-state franchise operation, Bookkeep helps you finally make sense of your numbers, and focus on growing your business, not wrangling spreadsheets.
