Shopify's pricing page shows a subscription number. That's the smallest of the fees you'll pay. A seller on the $39/month Basic plan doing $50,000 in monthly revenue actually pays Shopify closer to $1,500 once payment processing and apps are counted.
| Plan | Monthly | Card rate (online) | Best for |
|---|---|---|---|
| Starter | $5 | 5% + $0.30 | Selling via social only |
| Basic | $39 | 2.9% + $0.30 | New stores under $50K/mo |
| Shopify | $105 | 2.6% + $0.30 | $50K-$200K/mo |
| Advanced | $399 | 2.4% + $0.30 | $200K-$1M/mo |
| Plus | From $2,300 | Negotiable | $1M+/mo |
The processing fee compounds with every sale. A store doing $50,000 in monthly revenue on the Basic plan at 2.9% + $0.30 pays approximately $1,450 in percentage fees + $150 in per-transaction fees (on ~500 transactions) + $39 subscription = $1,639/month in Shopify fees alone (3.3% of revenue).
At $200,000/mo on the Shopify plan, the effective rate drops to about 2.9%. At $1M/mo on Advanced, it's about 2.6%.
If you use Stripe, PayPal, Amazon Pay, or any non-Shopify payment processor, Shopify charges a surcharge on top of whatever that processor charges: 2% on Basic, 1% on Shopify, 0.5% on Advanced, 0.15% on Plus. This is why most sellers default to Shopify Payments unless there's a specific reason to use another processor.
The typical ecommerce store runs 12-20 apps. Common ones: Klaviyo (email, $20-$500+/mo), Yotpo or Loox (reviews, $15-$250/mo), Recharge or Loop (subscriptions, $99-$1,000+/mo), Triple Whale (analytics, $99-$500/mo), Postscript (SMS, $25-$1,000+/mo), ShipStation ($9-$159/mo).
A growing store typically pays $400-$1,200/mo in app subscriptions.
| Line item | Amount | % of revenue |
|---|---|---|
| Shopify subscription (Shopify plan) | $105 | 0.04% |
| Payment processing (2.6% + $0.30 on 2,500 transactions) | $7,250 | 2.90% |
| App subscriptions | $800 | 0.32% |
| Shopify Shipping (mixed) | $3,200 | 1.28% |
| Total Shopify ecosystem fees | $11,355 | 4.54% |
4.5% of revenue paid to the Shopify ecosystem is fairly typical for a $200-500K/mo store. Larger stores on Advanced or Plus see this drop to 3.5-4%.
Each fee category posts to a different account: Subscription → Subscriptions/Software expense; Payment processing → Merchant fees; App subscriptions → Software expense; Shipping → Shipping expense; Chargebacks → Chargeback fees.
ConnectBooks parses Shopify settlements and posts each fee category to the right account automatically.
On standard plans, no. On Shopify Plus, yes. Rates are negotiable based on volume and contract length.
Yes. All Shopify subscription, payment processing, app, and shipping fees are deductible business expenses.
Basic plan + Shopify Payments + minimum apps + no Shopify Shipping. For a small store under $30K/mo, total cost is typically $50-$100/mo plus processing.
Get Shopify fees in your books automatically. ConnectBooks reconciles every Shopify fee category to the correct QuickBooks or Xero account in real time. 30-day free trial.
Running an e-commerce business comes with plenty of challenges, but ConnectBooks is here to make your life easier. With real-time insights, seamless integrations, and detailed tracking of your profitability and inventory, you can stay ahead of the game. Whether you’re selling on Amazon, Shopify, Walmart, TikTok or eBay, ConnectBooks helps you manage your finances with 100% accuracy and confidence, so you can focus on growing your business.
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