Shopify Bookkeeping Services
in Canada
Know what you sold, what Shopify paid out, and what your store kept.
Paperless Books reconciles Shopify Payments, PayPal, and other payment accounts in QuickBooks Online or Xero, so your monthly reports tie back to your store and bank.
Hamilton, Ontario · Online bookkeeping across Canada
Where Shopify Books Get Messy
The same order can show up in Shopify, a payment app, and your bank feed. Here’s where the numbers usually come apart.
Payouts That Don’t Match Sales
Shopify can group several orders in one deposit after fees, refunds, or other adjustments. Recording the bank deposit as sales hides what happened in between.
Returns and Chargebacks
A refund issued this month can reduce a later payout. Disputed payments can also create separate fees and reversals that need to be traced.
Shopify Gift Cards
Gift card sales and redemptions show up at different points. Tracking outstanding balances helps keep redeemed gift cards from being counted twice.
Inventory and Cost of Goods Sold
A large stock order can drain cash before the products sell. Your reports should show what’s still on hand and the cost of the items you’ve sold.
GST/HST at Checkout
Shopify’s tax report can differ from your books when refunds, point-of-sale transactions, or tax codes are handled inconsistently.
PayPal and Multiple Currencies
PayPal settlements and USD deposits can take a different route to your bank. Separate records help explain fees, transfers, and currency differences.
Shopify POS and Online Orders
In-store cash, card payments, and online orders settle differently. We trace each payment type so a POS sale and its bank deposit don’t both get recorded as revenue.
If you can’t explain the gap between Shopify sales and your bank deposits, start with one payout.
What Your Shopify Books Should Tell You
See What Your Store Actually Earned
Suppose customers paid $1,000, including $100 in sales tax. If the processor deducts $30 in fees before sending the deposit, $970 lands in your bank. The books still need to show $900 in sales, $100 in tax collected, and $30 in fees.
Once sales, refunds, and product costs are recorded consistently, you can see whether a busy month actually improved your margin. Payment fees, shipping, and ad spend show where the rest went.
From Shopify Order to Bank Deposit
We match Shopify’s payout detail to the bank and review money still with the processor at month-end. That gives you a way to tell an ordinary timing difference from an entry that needs fixing.
✔︎ Shopify Accounting Setup
Set up Shopify sales, taxes, fees, and payment clearing accounts in QuickBooks Online or Xero around the way your store takes payment.
✔︎ Payouts, Refunds, and Disputes
Tie payment activity to deposits and track refunds, chargebacks, and adjustments that move between payouts.
✔︎ Inventory and Supplier Costs
Record supplier bills and review inventory and cost of goods sold using the stock and cost records you have available.
✔︎ Monthly Reconciliation and Sales Tax
Reconcile bank, card, and processor accounts. Review GST/HST records and prepare or file applicable returns when included in your scope.
✔︎ Shopify Cleanup and Catch-Up
Rebuild missing months, correct duplicate sales, and investigate older payment balances before monthly bookkeeping begins.
What Shopify Bookkeeping Includes
Choose ongoing monthly bookkeeping, a catch-up project, or help sorting out your Shopify accounting setup.
Monthly Financial Reports & Store Margins
Review your profit and loss statement and balance sheet. See how discounts, returns, product costs, and operating expenses affected the month. If your records separate sales channels, we can discuss reporting by channel.
Shopify Bookkeeping Cleanup & Catch-Up
We compare store reports, processor records, and bank activity for the missing periods. Common fixes include payouts booked as new sales, refunds posted twice, and balances left in payment clearing accounts.
Shopify Payments & Bank Reconciliation
We match deposits to payout records, account for fees and adjustments, and review separately settled PayPal or Stripe activity where applicable. We carry forward supported amounts still in transit.
Canadian GST/HST Bookkeeping Support
We compare Shopify tax reports with the ledger, review how refunds are recorded, and flag discrepancies before filing. We can also organize records for applicable PST or QST and flag cross-border questions for your tax advisor.
Inventory & Cost of Goods Sold
Using your available supplier invoices and inventory records, we review what’s still on hand and what was sold. We can organize freight and duty records for review when you import stock.
Supplier Bills & Store Expenses
We record expenses such as Shopify subscriptions, fulfilment, packaging, and ad spend in categories you can compare month to month.
Shopify Integration & Sales Mapping
We review how store data reaches QuickBooks Online or Xero. If you use a connector, we check its sales, refund, fee, and tax mapping against actual payouts.
QuickBooks Online / Xero Troubleshooting
We investigate duplicated sales from app imports and bank feeds, old balances in clearing accounts, and payouts missing from your books.
What You Can See After Month-End
Know What Each Deposit Includes
Follow the sales, refunds, fees, and adjustments behind a bank deposit. If there’s a difference, you can see which report or transaction explains it.
See Cash Still With Your Processor
Review which payouts landed and which were still in transit at month-end. Flag held funds or older balances that need a closer look.
Understand Your Store’s Margin
See how returns, discounts, and the cost of the goods you sold affected gross profit. Review shipping, processing fees, and advertising separately to understand what’s left after operating costs.
Know Where the Month Stands
Get reconciled accounts and monthly financial reports. When your accountant needs year-end records, you can share the reports and supporting reconciliations.
Software We Work With
We work in QuickBooks Online or Xero and review how Shopify, payment processors, and receipt tools feed into the books. On the first call, tell us what you use today and where the numbers stop matching.
Accounting, receipts, and reports
Store and Sales Tools
Payroll
Payments and Money Movement
Bookkeeping for Growing Shopify Stores
Our monthly service is built for Canadian merchants, including stores doing $100,000+ in yearly
Built Around How You Sell
We Work With
- Online-only stores
- Online and in-store retailers
- Owner-operated shops
- Growing ecommerce teams
- Subscription brands
- Multi-channel sellers
Store Types
Shopify Stores
- Clothing and accessories
- Beauty and personal care
- Home goods
- Food and beverage
- Health and wellness
- Sporting goods
- Specialty retail
Tell us how you sell, take payments, and track inventory so we can scope the work around your store.
Meet Your Shopify Bookkeepers
Paperless Books is based in Hamilton, Ontario and has over 7 years of accounting and full-charge bookkeeping experience, including retail, and tax preparation.
Start With One Real Payout
We pick a recent deposit and follow it back to Shopify’s payout detail. That first check helps uncover duplicate income, fees coded to sales, or a payment channel missing from the books.
Certified in QuickBooks and Xero
QuickBooks ProAdvisor and certified Xero Advisor. We work with the accounting software you use and document how your store activity is recorded.
A Scope That Fits Your Store
We put the scope in writing based on your sales channels, payment processors, inventory records, reporting needs, and any months that need cleanup.
Client Testimonials
★★★★★
The perfect Accountant! He help me out with all my questions. I will recommend it and work again with him! Thank you so much Samuel. You are the best
Lucia
★★★★★
I needed someone to automate my shopify with Quickbooks. Samuel was able to do this and now I only spend 1 hour per month on bookkeeping. A lot better than the hours I spent trying to figure it all out.
Megan
★★★★★
Paperless Books helped me fix my quickbooks. It was a mess. Quickbooks is too complicated for me so I am grateful they were able to bring it up to date for me.
Kwame
How Online Shopify Bookkeeping Works
Start with a free consultation. You approve the scope before work starts.
Step 1 – Book a Free Consult
Tell us how you sell and get paid. Share your sales channels, software, last reconciled month, and any filing deadlines. We’ll confirm the scope and fee in writing before work starts.
Step 2 – Review Your Store and Books
We trace a recent payout. We check the sales reports, payment accounts, and accounting file together. Then we flag missing periods, duplicate imports, and any records we’ll need from you.
Step 3 – Close the Books Monthly
Get reconciled books and monthly reports. We reconcile the accounts in scope, flag items that need your input, and send your reports. At year-end, we can share the reconciled books and supporting records with your accountant.
Hamilton-Based Shopify Bookkeeping Across Canada
Paperless Books works online with Shopify merchants in Hamilton, Toronto, and across Ontario and Canada.
Frequently Asked Questions
Why don’t my Shopify sales match my bank deposits?
Shopify Payments can group several transactions into a single deposit. Fees, refunds, chargebacks, adjustments, and payout timing can all change the amount that reaches the bank.
We use Shopify’s payout records to explain the difference and match the net payout to the bank statement.
What kinds of Shopify stores do you work with?
We work with Canadian Shopify merchants selling online, through Shopify POS, or across multiple channels. Tell us which gateways and sales channels you use so we can confirm what’s in scope.
Can you catch up on overdue Shopify bookkeeping?
Yes.
We compare Shopify sales and processor reports with your bank statements and ledger. We can correct duplicate deposits, rebuild missing months, and review older balances before starting monthly work.
Are software and connector fees included?
Most clients pay for their accounting software separately. We confirm any connector or software costs when we put together your quote.
Can you do my Shopify bookkeeping in QuickBooks Online or Xero?
Yes. We work in both QuickBooks Online and Xero.
We review how Shopify sales, tax, refunds, and fees are being posted and check that payouts can be matched to your bank.
If a connector is already running, we test its entries against actual transactions before changing the setup.
How do you handle inventory and cost of goods sold?
We use your available supplier invoices and stock records to review inventory and cost of goods sold. If landed costs or inventory adjustments need more detail, we identify the records needed before quoting the work.
How do I share access to Shopify and my books?
We agree on which Shopify reports and accounting permissions are needed. During onboarding, we show you how to grant access and share records through the client portal.
Is monthly bookkeeping a long-term commitment?
Ongoing bookkeeping is month to month. Your engagement letter sets out the scope, billing, and cancellation terms.
Can you reconcile Shopify POS and PayPal?
We can include Shopify POS and separately settled payments such as PayPal in your scope.
We review the sales and settlement reports for each channel, including cash or other payment methods that don’t appear in a Shopify Payments payout.
Can you help with GST/HST for my Canadian Shopify store?
We reconcile GST/HST records against store reports and the ledger, organize supporting records, and flag tax-code or refund differences. Preparation or filing can be included in your agreed scope.
How much does Shopify bookkeeping cost?
Pricing depends on the number of sales channels and payment accounts, transaction volume, reporting detail, and how far behind the books are. After the free consultation, we confirm your monthly fee and any separate cleanup cost in writing.