At a Glance
Multi-channel ecommerce accounting is one of the most common areas where Canadian online sellers fall behind. If you sell on Shopify, Amazon, Etsy, and wholesale simultaneously, each platform reports differently, charges different fees, collects taxes under different rules, and deposits money on different schedules. Without a consolidated accounting system, you cannot answer the most important question in your business: which channels are actually profitable?
This guide walks through the exact workflow we use at LedgerLogic to consolidate multi-channel sellers into a single, accurate set of books. It builds on our e-commerce accounting framework for Canadian sellers and applies it to the specific complexity of operating across multiple sales platforms. Whether you sell on two channels or six, the principles are the same.
Affiliate Disclosure: LedgerLogic is a partner of A2X, Synder, Xero, and Dext. We may earn a commission if you sign up through our links at no extra cost to you. We only recommend tools we use with our own clients.
Selling on Multiple Platforms?
Our CPA team consolidates Shopify, Amazon, Etsy, and wholesale accounting into one clean set of books in Xero. We set up channel-level profitability reporting so you know exactly where your margin comes from.
The Multi-Channel Accounting Challenge
The fundamental problem with selling on multiple platforms is that each one treats your money differently. Understanding these differences is the first step toward building a consolidated accounting system.
Shopify Payments sends net payouts to your bank every 1–3 business days. Each payout bundles gross sales, refunds, Shopify fees, and shipping charges into a single deposit. Without middleware, you cannot see the component parts. For a deep dive on Shopify-specific bookkeeping, see our Shopify bookkeeping guide.
Amazon Seller Central sends biweekly settlement reports. These reports deduct FBA fees, referral fees, advertising costs, and storage fees before depositing the net amount. The fee structure is significantly more complex than Shopify, and Amazon withholds funds during the settlement period. Our Amazon FBA accounting guide covers the full breakdown.
Wholesale and B2B customers typically pay on net-30 invoices. Unlike platform sales, wholesale revenue is recognised on the invoice date under accrual accounting, with the cash arriving weeks later. This creates accounts receivable balances that do not exist with platform sales.
Etsy, Stripe, and PayPal each have their own payout schedules, fee structures, and reporting formats. Etsy charges listing fees, transaction fees, and payment processing fees. Stripe and PayPal charge per-transaction fees and deposit on their own schedules.
Currency differences add another layer. If you sell on Amazon.com in USD and on Shopify in CAD, every Amazon transaction creates a foreign exchange gain or loss that must be tracked in your books.
Inventory splits across FBA warehouses, your own storage, and wholesale allocation make it difficult to know your true inventory position at any given time.
The result: without a deliberate consolidation strategy, you end up with financial data scattered across six different dashboards, none of which agree with each other, and no way to produce a reliable P&L.
Consolidating Revenue from Multiple Channels
The solution is a single source of truth. We use Xero as the central accounting platform for all multi-channel clients. Every sales channel, regardless of its native reporting, flows into Xero through dedicated middleware connectors.
Xero as the hub. Xero handles multi-currency, unlimited bank feeds, and robust tracking categories natively. It is the accounting software best suited to multi-channel e-commerce in Canada.
A2X for Shopify. A2X connects Shopify to Xero and creates summary journal entries that break each payout into gross sales, refunds, fees, shipping, and taxes. This is the same tool we use for single-channel Shopify sellers, and it works identically in a multi-channel setup.
A2X for Amazon (separate subscription). A2X offers a separate product specifically for Amazon. It parses Amazon settlement reports and creates Xero journal entries that map FBA fees, referral fees, advertising costs, and net sales into the correct accounts. Note that A2X for Shopify and A2X for Amazon are different subscriptions with different pricing.
Synder for additional channels. Synder handles Etsy, Stripe, and PayPal in a single connector. It can also handle Shopify and Amazon, making it a viable single-tool alternative for sellers who prefer simplicity over the granularity that A2X provides.
Xero invoicing for wholesale. For B2B and wholesale customers, create invoices directly in Xero. This keeps wholesale revenue in the same system as platform revenue, with proper accounts receivable tracking.
Chart of accounts structure. All channels flow into the same chart of accounts, but you need separate revenue and COGS accounts per channel — or use Xero tracking categories to tag transactions by channel. See our e-commerce chart of accounts guide for the recommended account structure.
CPA Pro Tip: We recommend separate revenue accounts per channel (e.g., "4100 — Gross Sales — Shopify", "4110 — Gross Sales — Amazon", "4120 — Gross Sales — Wholesale") rather than tracking categories alone. Separate accounts appear directly on your P&L without needing to run filtered reports, which makes monthly reviews faster and reduces the chance of missing a channel.
Channel-Level Profitability Reporting
Total profit and loss statements hide the story. A multi-channel seller with $500,000 in combined revenue might assume the business is healthy because overall margins are reasonable. But when you break it down by channel, the picture often changes dramatically.
Consider this simplified example for a Canadian seller operating on three channels:
| Metric | Shopify | Amazon | Wholesale |
|---|---|---|---|
| Gross Revenue | $120,000 | $280,000 | $100,000 |
| COGS | $48,000 | $112,000 | $55,000 |
| Platform Fees | $3,600 | $42,000 | $0 |
| Advertising | $18,000 | $28,000 | $2,000 |
| Shipping/Fulfilment | $12,000 | $33,600 | $8,000 |
| Net Profit | $38,400 | $64,400 | $35,000 |
| Net Margin | 32% | 23% | 35% |
In this example, Amazon drives the highest volume but the lowest margin. Shopify and wholesale both deliver higher margins with lower revenue. Without per-channel reporting, the seller might pour more advertising spend into Amazon assuming it is the growth engine, when in fact Shopify and wholesale deliver more profit per dollar of revenue.
To generate this view in Xero, you need either separate revenue and COGS accounts per channel or Xero tracking categories applied to every transaction. A2X and Synder both support mapping to channel-specific accounts, making this automatic once configured. Run a monthly P&L by channel to see exactly where your margin comes from.
Inventory Across Multiple Channels
Inventory management becomes significantly more complex when you sell on multiple platforms. The core risk is overselling: if the same product is listed on Shopify, Amazon, and your wholesale catalogue, a spike in orders on one channel can sell through stock that was promised to another.
FBA inventory is physically held in Amazon's warehouses. You ship units to FBA, and Amazon handles picking, packing, and shipping. This inventory is separate from your self-fulfilled stock, and Amazon charges storage fees that increase if units sit too long.
Self-fulfilled inventory covers orders from Shopify and any other channel where you handle shipping yourself. This stock is in your own warehouse or third-party logistics (3PL) provider.
Wholesale allocation requires reserving inventory for B2B orders, which are typically larger quantities with longer lead times.
The accounting challenge is ensuring your total inventory value in Xero reflects the sum of all three pools. Each month, reconcile your FBA inventory report, your self-fulfilled count, and your wholesale allocation to confirm the total matches your balance sheet. For detailed COGS calculation methods, see our e-commerce COGS guide.
For sellers with high SKU counts or complex allocation needs, dedicated inventory management tools like Cin7 or Dear Inventory can sync stock levels across platforms in real time and push inventory adjustments into Xero automatically.
Tech Stack for Multi-Channel Accounting
Here is the complete software stack we configure for multi-channel sellers at LedgerLogic. Each tool serves a specific purpose, and they work together to create a fully automated accounting workflow.
| Tool | Purpose | Monthly Cost (approx.) |
|---|---|---|
| Xero | Core accounting, GST/HST, bank reconciliation | $50–$92 CAD |
| A2X for Shopify | Automated Shopify payout reconciliation | $19–$69 USD |
| A2X for Amazon | Automated Amazon settlement reconciliation | $19–$69 USD |
| Synder | Etsy, Stripe, PayPal reconciliation | $53–$160 USD |
| Dext | Receipt and expense capture | $24–$66 CAD |
Important note on A2X pricing: A2X for Shopify and A2X for Amazon are separate subscriptions. If you sell on both platforms, you will pay for two A2X accounts. This is one of the reasons some sellers prefer Synder, which can handle multiple channels in a single subscription. However, in our experience, A2X provides more accurate and CPA-friendly journal entries for Shopify and Amazon specifically. Explore our full e-commerce accounting tools comparison for a detailed breakdown of each option.
CPA Pro Tip: Start with A2X for your two highest-volume channels (usually Shopify and Amazon) and use Synder for everything else. This gives you the best accuracy where it matters most while keeping costs manageable. As revenue grows, you can evaluate whether to move additional channels to dedicated connectors.
GST/HST for Multi-Channel Sellers
GST/HST compliance is where multi-channel accounting gets particularly nuanced in Canada. Each sales channel handles tax collection differently, but all of it must be reconciled on a single GST/HST return.
Amazon as marketplace facilitator. Since July 2021, Amazon collects and remits GST/HST on behalf of third-party sellers for sales to Canadian customers, as required under the CRA's digital economy GST/HST rules. This means the GST/HST on Amazon sales does not flow through your books in the traditional sense — Amazon handles the remittance directly. Your accounting must reflect this correctly: Amazon revenue is recorded net of the marketplace-facilitated tax.
Shopify: you collect and you remit. Shopify calculates the correct GST/HST at checkout based on your customer’s province, but you are responsible for remitting it to the CRA. The tax collected flows through your Shopify payouts, and A2X or Synder separates it into the correct tax liability accounts in Xero.
Wholesale B2B transactions. If you sell to GST/HST-registered businesses, the sale may be zero-rated or the buyer may provide their GST/HST number. You still need to issue invoices with the correct tax treatment and report these transactions on your return.
One return, multiple sources. Regardless of how many channels you sell on, you file one GST/HST return. Xero aggregates the tax collected across all channels and subtracts your input tax credits (ITCs) on business expenses to calculate the net amount owing. When A2X and Synder are configured correctly, the tax accounts in Xero contain all the data you need for an accurate filing. For the complete framework, see our e-commerce GST/HST guide.
When Multi-Channel Means You Need a CPA
Some multi-channel sellers manage their own books effectively. Most reach a complexity threshold where the cost of mistakes exceeds the cost of professional help.
Three or more active sales channels. Each additional channel adds a connector, a fee structure, a reconciliation workflow, and a set of tax rules. The compound complexity grows faster than most sellers expect.
Combined revenue exceeding $200,000. At this revenue level, the CRA pays closer attention. Inaccurate GST/HST reporting, missing income from a channel, or incorrect expense classification can trigger a review or audit. The cost of defending an audit far exceeds the cost of getting the books right from the start.
Multi-currency transactions. Selling in USD on Amazon.com while operating a CAD Shopify store creates foreign exchange gains and losses on every settlement. These must be tracked and reported correctly.
Inventory complexity. If you carry significant inventory across FBA, self-fulfilled, and wholesale pools, the COGS calculation and inventory valuation require careful attention. Errors in COGS directly distort your profitability picture.
Time cost of DIY. Multi-channel bookkeeping done properly takes 8–15 hours per month for a moderately complex business. If your time is better spent on product development, marketing, or customer relationships, outsourcing the books is a straightforward ROI calculation.
Our e-commerce accounting team specialises in multi-channel consolidation. We set up the full tech stack, configure channel-level reporting in Xero, handle GST/HST filing, and provide monthly financial reviews so you know exactly how each channel performs.
Frequently Asked Questions
Seb ProstCPA, Ex-CRA
Licensed CPA with 10+ years of experience, including work with the Canada Revenue Agency. Founder of LedgerLogic, a cloud accounting firm serving Canadian SMEs. Xero Certified Advisor.
