Bookkeeping for Shopify Stores in Canada
Shopify bookkeeping requires more than recording deposits. Shopify Payments payouts do not match your actual sales. Payment processing fees, refunds, chargebacks, discounts, shipping collected, taxes collected and app subscription costs are all netted against your payout. We break every payout down to the penny, track inventory with landed costs, file HST correctly and deliver monthly financials that show your true margins. From $150/month. T2 filed FREE.
AFFORDABLE Bookkeeping Built for the Shopify Business Model
We work with Canadian Shopify store owners who have discovered that their bank deposits do not match their Shopify sales. That is because Shopify nets payment processing fees, refunds, chargebacks and adjustments against your payout before depositing it. A $10,000 sales day results in a $9,420 deposit after Shopify Payments takes its 2.9% + $0.30 per transaction. If your bookkeeper records $9,420 as revenue, your financials are wrong from the first entry.
We record gross revenue, payment processing fees, refunds, discounts, shipping collected, taxes collected and net payout as separate line items. Inventory is tracked with landed costs. HST is filed with every ITC claimed. Monthly P&L shows your true gross margin, not the deposit amount. For a full overview, visit our Shopify accounting and bookkeeping page.
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Why Shopify Store Bookkeeping Is Different from Standard Bookkeeping
| Shopify Challenge | What Goes Wrong Without Specialized Bookkeeping | What We Do |
|---|---|---|
| Shopify Payments payout reconciliation | Your bookkeeper records the bank deposit as revenue. The deposit is net of payment fees, refunds and adjustments. Revenue is understated by 3% to 8%. Expenses are missing entirely. | We reconcile every Shopify payout: gross sales, payment processing fees (2.4% to 2.9% + $0.30), refunds, chargebacks, shipping collected, taxes collected and net deposit. Each component recorded separately. |
| Multiple payment gateways (Shopify Payments, PayPal, Stripe, Shop Pay Instalments) | Each gateway deposits at different times with different fee structures. PayPal holds funds. Stripe deposits daily. Shop Pay Instalments pays over time. Revenue timing is wrong and fees are not tracked per gateway. | We reconcile each payment gateway independently. Fees tracked per gateway. Revenue recognized when the order is placed, not when the deposit arrives. Gateway-specific fee reports delivered monthly. |
| HST collected by Shopify vs. your HST return | Shopify collects HST at checkout based on your tax settings. If your tax settings are wrong, you collect too much or too little. Your HST return does not match what Shopify collected. CRA assesses the difference. | We verify Shopify tax settings at onboarding. HST collected on orders is reconciled against your HST return every period. ITCs claimed on all eligible business expenses. Discrepancies identified and corrected before filing. |
| Discounts, gift cards and promotional pricing | Discount codes reduce the selling price but many bookkeepers record the full price as revenue and then have no matching expense for the discount. Gift card redemptions are recorded as revenue when redeemed instead of when the gift card was sold (the liability). Revenue is overstated. | Discounts tracked as a contra-revenue line item (reducing gross revenue to net revenue). Gift cards recorded as a liability when sold and recognized as revenue only when redeemed. Promotional pricing adjustments visible in monthly reporting. |
| Shipping collected and shipping expense | Shipping charges collected from customers are mixed into revenue. Shipping costs paid to Canada Post, UPS, FedEx or Shopify Shipping are categorized as a general expense. The net shipping position (profit or loss on shipping) is invisible. | Shipping collected from customers tracked as a separate revenue line. Shipping expense tracked separately. Net shipping position (collected minus paid) reported monthly. Many Shopify stores lose $2,000 to $8,000/year on shipping without knowing it. |
| Inventory valuation and COGS | Inventory is not tracked. COGS is estimated or missing. Products purchased from suppliers are expensed immediately instead of capitalized. Gross margin is unknown or inaccurate. Year-end inventory count does not match the books. | Inventory tracked using FIFO or weighted average. Landed cost includes product price + freight + duties + customs brokerage. COGS calculated per unit sold. Unsold inventory is a balance sheet asset. Year-end inventory reconciled to physical count. |
| Returns and refunds | Refunds reduce the bank deposit but COGS is not reversed. Returned inventory is not added back to stock. COGS is overstated and inventory counts are wrong. | Refunds tracked as a separate contra-revenue line. COGS reversed on returned units. Inventory added back to stock. Refund rate calculated by product, by channel and by month. |
| Shopify app subscriptions and SaaS costs | Shopify charges a monthly subscription ($39 to $399 for Basic to Advanced). Third-party apps (email marketing, reviews, upsells, inventory management) add $50 to $500/month. These recurring costs are not tracked or are lumped into one "software" category. | Shopify subscription tracked as a fixed operating expense. Each app subscription categorized by function (marketing, operations, shipping, inventory). Total SaaS spend reported monthly so you can evaluate ROI on every app. |
What Is Included in Our Shopify Store Bookkeeping
| Service | What We Do |
|---|---|
| Shopify payout reconciliation | Every payout broken down: gross sales, payment processing fees, refunds, chargebacks, shipping collected, taxes collected and net deposit. Reconciled to your bank account. Discrepancies identified immediately. |
| Payment gateway fee tracking | Shopify Payments (2.4% to 2.9% + $0.30), PayPal, Stripe and any other gateway fees tracked separately. Monthly fee totals and percentage of revenue calculated per gateway. |
| Revenue recognition (gross vs. net) | Gross revenue recorded at the order total. Discounts, refunds, chargebacks and fees recorded as separate deductions. Net revenue visible on the P&L. Your true top-line revenue is always clear. |
| Inventory valuation and COGS | Inventory tracked using FIFO or weighted average with full landed costs (product + freight + duties + brokerage). COGS calculated per unit sold. Unsold inventory carried as a balance sheet asset. Year-end count reconciled. |
| HST filing | HST return prepared and filed every period. Shopify-collected HST reconciled against the return. ITCs claimed on all eligible expenses: payment gateway fees, shipping costs, app subscriptions, packaging, office rent, advertising. Quick Method vs. Regular Method analyzed annually. |
| Shipping cost analysis | Shipping collected from customers and shipping paid to carriers tracked as separate lines. Net shipping position reported monthly. Identifies whether your shipping rates cover your actual costs or whether you are losing money on every shipment. |
| Discount and gift card tracking | Discounts as contra-revenue. Gift cards as liability when sold, revenue when redeemed. Promotional campaigns tracked by code so you can see the ROI of each promotion. |
| App subscription and SaaS cost tracking | Every Shopify app and SaaS subscription categorized by function: marketing, shipping, reviews, inventory, analytics. Monthly total reported. Cost per app visible so you can cancel underperforming subscriptions. |
| Monthly financial statements | P&L, balance sheet and cash flow delivered monthly. Revenue by channel (if multi-channel), gross margin, payment fees as percentage of revenue, net shipping position, COGS by product line, net profit after all Shopify costs. |
| T2 corporate tax return | Filed FREE for every bookkeeping client. Financial statements, T2, GIFI, all CRA schedules, e-filing and CRA audit support included at no additional charge. |
Shopify Store Bookkeeping from $150/Month. T2 Filed FREE.
Payout reconciliation, inventory, HST, payment fees, shipping analysis, monthly financials. Fixed flat fee.
Shopify Store Bookkeeping: Real Client Results
DTC Fashion Brand, Shopify + Instagram
A Canadian direct-to-consumer fashion brand doing $280,000/year on Shopify was recording bank deposits as revenue. Payment processing fees ($8,120/year), refunds ($14,200) and discount codes ($11,400) were invisible. We set up proper gross-to-net revenue tracking, discovered the true gross margin was 42% (not the 58% the owner believed) and identified $3,200 in annual shipping losses (free shipping threshold set too low). The owner raised the free shipping threshold from $50 to $75, eliminating the shipping loss.
Health Supplement Store, Shopify + Amazon
A multi-channel supplement seller on Shopify and Amazon.ca was mixing both channels into one revenue account. Shopify Payments fees, Amazon referral fees and FBA fees were all categorized as "bank charges." Inventory was not tracked per channel. We separated the channels, tracked fees per platform, implemented FIFO inventory with landed costs (the supplements were imported from the US with duties) and delivered channel-specific P&L reports. Shopify was 34% margin. Amazon was 19% margin. The owner shifted ad budget to Shopify.
Home Decor Store, Shopify + Retail POS
A Canadian home decor brand selling through Shopify online and Shopify POS in a retail location was not reconciling online vs. in-store sales. Gift cards sold in-store and redeemed online (and vice versa) were creating double-counted revenue. Inventory was tracked in Shopify but not in QBO. We integrated Shopify with QBO, separated online and retail revenue streams, implemented gift card liability tracking and reconciled inventory between Shopify counts and QBO. The monthly financials now show profitability per channel with accurate inventory valuation.
New Shopify Store, First Year
A new Shopify store launching with $22,000 in startup inventory and $4,800 in app subscriptions had no bookkeeping system. We set up QBO from day one with a Shopify-specific chart of accounts, connected Shopify Payments and bank feeds, registered for HST voluntarily (to claim ITCs on startup inventory and expenses), tracked all app subscriptions by category and delivered monthly financials from month one. The seller claimed $4,160 in ITCs on startup costs in the first filing period.
How Shopify Store Bookkeeping Works
Connect
We connect to your Shopify admin, payment gateways, bank accounts and supplier records. Payout data flows into QBO automatically. Inventory counts synced.
Categorize
Every payout is broken down: gross sales, fees per gateway, refunds, chargebacks, discounts, shipping collected, taxes collected. Inventory purchases capitalized with landed costs.
Reconcile
Shopify payouts matched to bank deposits. Payment gateway statements verified. HST collected reconciled against your HST return. ITCs claimed on every eligible expense.
Report
Monthly P&L with gross margin, payment fee analysis, shipping position, COGS by product line, inventory valuation and cash flow. Year-end ready for your T2.
Every Shopify Cost We Track in Your Books
| Cost Category | What It Is | Typical Range | How We Track It |
|---|---|---|---|
| Shopify Payments processing fee | Credit card processing fee on every online transaction. | 2.4% to 2.9% + $0.30 per transaction (varies by Shopify plan) | Extracted from every payout. Monthly total and percentage of gross revenue calculated. Compared across plans to confirm you are on the right Shopify tier. |
| Third-party payment gateway fee | Additional fee if you use PayPal, Stripe or another gateway alongside Shopify Payments. | 0.5% to 2.0% additional transaction fee (Shopify charges this on top of the gateway's own fee) | Tracked per gateway. Monthly cost by gateway. Helps you decide whether to consolidate to Shopify Payments or keep multiple gateways. |
| Shopify subscription | Monthly platform subscription. | Basic $39/month. Shopify $105/month. Advanced $399/month. Plus: custom pricing. | Fixed operating expense tracked monthly. Plan level reviewed annually based on transaction volume (higher plans have lower processing fees). |
| App subscriptions | Third-party Shopify apps for email marketing, reviews, upsells, inventory, shipping, analytics. | $50 to $500+/month combined (depends on number and type of apps) | Each app categorized by function: marketing, operations, shipping, reviews, analytics. Monthly total reported. ROI evaluated per app. |
| Shipping costs (carrier) | Actual shipping cost paid to Canada Post, UPS, FedEx, Shopify Shipping or third-party fulfilment. | $3 to $15+ per order (varies by weight, destination, carrier) | Tracked as a separate expense. Compared against shipping collected from customers. Net shipping position (profit or loss) reported monthly. |
| Packaging and supplies | Boxes, poly mailers, tissue paper, branded inserts, tape, labels. | $0.50 to $3.00+ per order | Tracked as a COGS component or separate operating expense (depending on materiality). Per-order packaging cost calculated. |
| Advertising (Meta, Google, TikTok) | Paid advertising spend driving traffic to your Shopify store. | Varies. Typically 15% to 35% of revenue for growth-stage stores. | Tracked as marketing expense by platform. ROAS (Return on Ad Spend) calculated per channel. Monthly ad spend vs. attributed revenue reported. |
| Shopify POS hardware/software (if retail) | Shopify POS subscription and hardware (card reader, terminal, cash drawer). | POS Pro $89/month per location. Hardware $49 to $459. | POS subscription as fixed expense. Hardware as capital asset (CCA) or expense depending on cost. In-store and online revenue tracked separately. |
HST for Canadian Shopify Stores: What You Need to Know
| Scenario | HST Treatment | What We Do |
|---|---|---|
| Shopify sales to Canadian customers | You must collect HST at the customer's provincial rate (13% Ontario, 5% Alberta, 12% BC, etc.). Shopify calculates and adds HST at checkout based on your tax settings. You are responsible for the accuracy of the tax collected. | We verify your Shopify tax settings at onboarding. HST collected is reconciled against your HST return every period. Any discrepancy is identified and corrected before filing. |
| Shopify sales to US customers | Zero-rated exports. No Canadian HST collected. You charge $0 HST on orders shipped to the US. Full ITCs on all Canadian expenses are still claimable. | We zero-rate all US orders. Full ITCs claimed on Canadian expenses (inventory, shipping, advertising, apps, office, packaging). Sellers with 30%+ US revenue are frequently in a net ITC refund position. |
| ITCs on Shopify Payments processing fees | Shopify Payments is processed by Shopify (a Canadian entity for tax purposes). HST is included in the processing fee. This HST is recoverable as an ITC. | We extract the HST component from processing fees and claim it as an ITC. On $12,000/year in Shopify Payments fees, the recoverable HST is approximately $1,381. |
| ITCs on Shopify subscription and app fees | Shopify subscription and many Canadian-billed app subscriptions include HST. Recoverable as ITCs. | We track HST on every Shopify and app invoice. On $6,000/year in combined subscription and app costs, the recoverable HST is approximately $691. |
| ITCs on advertising (Meta, Google) | Meta and Google charge HST on ads served to Canadian businesses (registered for HST). Recoverable as ITCs. | We claim ITCs on all advertising spend. On $40,000/year in Meta and Google ads, the recoverable HST is $4,602. |
| ITCs on shipping and packaging | HST paid on shipping (Canada Post, UPS, FedEx) and packaging supplies purchased from Canadian vendors is fully recoverable. | We track HST on every shipping invoice and packaging purchase. On $15,000/year in shipping and packaging, the recoverable HST is $1,726. |
| Quick Method vs. Regular Method | Shopify stores with low COGS (digital products, print-on-demand, dropshipping) may save with Quick Method (8.8%). Stores with high COGS (physical inventory purchased from suppliers) almost always save more with Regular Method. | We calculate both methods annually. Physical product stores with inventory, shipping and advertising costs almost always benefit from Regular Method because ITCs on purchases, fees and advertising exceed the Quick Method savings. |
Total Missed ITCs Can Exceed $8,400/Year: Shopify Payments fees ($1,381) + subscription and app fees ($691) + advertising ($4,602) + shipping and packaging ($1,726) = $8,400 in recoverable HST on a Shopify store with $200,000 in revenue. Most Shopify store owners who self-file their HST claim zero ITCs or only a fraction. We claim every eligible ITC for every Shopify client. For the full scope of our Shopify services, visit our Shopify accounting and bookkeeping page.
Shopify Store Bookkeeping Pricing
| Shopify Revenue | Monthly Bookkeeping Fee | What Is Included |
|---|---|---|
| Under $100,000/year | From $150/month | Payout reconciliation, payment fee tracking, inventory (basic), HST filing, bank reconciliation, monthly financials, T2 filed FREE |
| $100,000 to $300,000/year | From $250/month | Everything above + detailed inventory valuation (FIFO), multi-gateway fee analysis, shipping cost analysis, discount/gift card tracking, app cost categorization |
| $300,000 to $500,000/year | From $400/month | Everything above + per-product profitability, multi-channel P&L (if Shopify + Amazon/wholesale), ROAS reporting, quarterly tax planning review |
| $500,000 to $1,500,000/year | From $600/month | Everything above + dedicated CPA, monthly review meeting, cash flow forecasting, supplier payment scheduling, growth analysis |
| Over $1,500,000/year | From $900/month | Full-service: weekly reporting, multi-channel, inventory management, tax planning, payroll if applicable, Shopify POS integration |
T2 Filed FREE for Every Shopify Bookkeeping Client: Your T2 corporate tax return is included at no additional charge with every bookkeeping plan. Financial statements, T2, GIFI, all CRA schedules, e-filing and CRA audit support. No extra invoice at year-end.
Frequently Asked Questions: Bookkeeping for Shopify Stores
Meet Your Shopify Store Bookkeeping Experts
Your Shopify books are managed and reviewed by licensed CPAs who understand e-commerce payout structures, inventory costing and multi-channel compliance.
Sharad Gondaliya, CPA
Founder and Principal CPA. Oversees Shopify store bookkeeping. Specializes in payout reconciliation, multi-channel tracking, inventory valuation, HST compliance for e-commerce and T2 preparation for Shopify businesses.
Vandana Goel, CPA
Senior CPA. Manages bookkeeping for Shopify and multi-channel e-commerce sellers. Experienced in payment gateway reconciliation, landed cost inventory tracking, gift card liability accounting and channel-specific profitability reporting.
What Our Clients Say
900+ five-star reviews from business owners across Ontario and Canada.
Shopify Store Bookkeeping from $150/Month. T2 Filed FREE.
We reconcile every Shopify payout, track every fee, value your inventory, file your HST and deliver monthly financials that show your true margins. 900+ five-star reviews.