Shopify Profit Calculator: Track Real Margins After All Fees (2025)

Your Shopify dashboard shows $50,000 in sales this month. Exciting, right?

But here's what actually hit your bank account: $32,500.

Where did $17,500 go? Let me show you the 7 different fees eating into your Shopify profits - and how to calculate your real margins.

The Real Cost of Running a Shopify Store

Shopify doesn't just charge you a monthly subscription fee. There are multiple layers of costs that compound on every single sale:

The fees most Shopify sellers pay:

1. Shopify subscription ($39-399/month)
2. Shopify transaction fees (0.5-2% depending on plan)
3. Payment processing fees (2.9% + $0.30 or more)
4. Shopify app fees ($10-200+/month)
5. Product costs (wholesale, manufacturing, or dropshipping)
6. Shipping costs (or "free shipping" you absorb)
7. Marketing costs (Facebook ads, Google ads, influencers)

Let's break down each one and calculate your real profit.

Shopify Fee Structure (2025 Breakdown)

1. Shopify Subscription Plans

Basic Shopify: $39/month

• 2.9% + $0.30 per online transaction
• 2.7% per in-person transaction
• No transaction fee if using Shopify Payments
• 2% transaction fee if using third-party payment gateway

Shopify: $105/month

• 2.7% + $0.30 per online transaction
• 2.5% per in-person transaction
• No transaction fee if using Shopify Payments
• 1% transaction fee if using third-party payment gateway

Advanced Shopify: $399/month

• 2.5% + $0.30 per online transaction
• 2.4% per in-person transaction
• No transaction fee if using Shopify Payments
• 0.5% transaction fee if using third-party payment gateway

Shopify Plus: $2,300+/month (enterprise)

• 2.15% + $0.30 per online transaction
• Negotiable rates for high volume

2. The Hidden Transaction Fee Trap

Here's something that confuses many sellers: You pay transaction fees TWICE if you don't use Shopify Payments.

Example using PayPal instead of Shopify Payments:

$100 sale on Basic Shopify:

• PayPal fee: $3.20 (2.9% + $0.30)
• Shopify transaction fee: $2.00 (2% because you're not using Shopify Payments)
• Total fees: $5.20 (5.2%)

Same sale using Shopify Payments:

• Shopify Payments fee: $3.20 (2.9% + $0.30)
• No additional transaction fee
• Total fees: $3.20 (3.2%)

This is why Shopify heavily pushes Shopify Payments - it's actually cheaper for you AND locks you into their ecosystem.

3. App Fees That Add Up Fast

Most Shopify stores use 5-15 apps. Here's what they typically cost:

Common app categories and costs:

• Email marketing (Klaviyo, Omnisend): $20-300/month
• Reviews (Judge.me, Loox): $15-50/month
• Upsells (Zipify, ReConvert): $10-100/month
• Inventory management: $30-200/month
• Customer support (Gorgias): $60-300/month
• SEO/Marketing: $20-100/month
• Subscriptions (Recharge): $40-300/month

Average app spend for successful stores: $150-500/month

Many sellers don't realize these recurring costs until they add up their expenses at year-end.

Calculate Your Shopify Profit (Step-by-Step)

Let's walk through a real example:

Example Store Breakdown

Monthly revenue: $50,000 Products sold: 500 units at $100 average order value Business model: Dropshipping with print-on-demand

Step 1: Subtract Shopify fees

• Plan: Basic Shopify = $39/month
• Payment processing (2.9% + $0.30 × 500 orders): $1,600
• Total Shopify fees: $1,639

Step 2: Subtract app fees

• Email marketing: $100
• Reviews app: $20
• Upsell apps: $50
• Customer service: $100
• Analytics: $30
• Total app fees: $300

Step 3: Subtract product costs

• Cost per unit: $40
• 500 units × $40 = $20,000
• Total COGS: $20,000

Step 4: Subtract shipping costs

• Offering "free shipping" to customers
• Actual shipping cost per order: $6
• 500 orders × $6 = $3,000
• Total shipping: $3,000

Step 5: Subtract marketing costs

• Facebook ads: $10,000
• Influencer partnerships: $2,000
• Total marketing: $12,000

Step 6: Calculate net profit

• Revenue: $50,000
• Shopify fees: -$1,639
• App fees: -$300
• Product costs: -$20,000
• Shipping: -$3,000
• Marketing: -$12,000
• Net profit: $13,061

Profit margin: 26.1%

Your dashboard says $50,000, but you actually made $13,061.

Profit Calculator by Business Model

Different Shopify business models have different cost structures:

Dropshipping Model

Typical margins: 15-25%

Revenue: $30,000

• Product cost (60% of revenue): -$18,000
• Shopify + payment fees (3.5%): -$1,050
• Apps: -$200
• Shipping markup: +$500 (you charge more than it costs)
• Marketing (25% of revenue): -$7,500
• Net profit: $3,750 (12.5% margin)

Reality check: Dropshipping has thin margins. You need volume to make real profit.

Print-on-Demand

Typical margins: 20-35%

Revenue: $20,000

• Product cost (50% of revenue): -$10,000
• Shopify + payment fees (3.5%): -$700
• Apps: -$150
• Shipping: -$0 (built into product cost)
• Marketing (20% of revenue): -$4,000
• Net profit: $5,150 (25.8% margin)

Better margins than dropshipping, but still marketing-heavy.

Wholesale/Retail Model

Typical margins: 40-60%

Revenue: $60,000

• Product cost (30% of revenue): -$18,000
• Shopify + payment fees (3.5%): -$2,100
• Apps: -$400
• Shipping: -$3,000
• Marketing (15% of revenue): -$9,000
• Inventory storage: -$500
• Net profit: $27,000 (45% margin)

Best margins, but requires upfront inventory investment and storage costs.

Digital Products

Typical margins: 85-95%

Revenue: $15,000

• Product cost (near zero): -$0
• Shopify + payment fees (3.5%): -$525
• Apps (minimal): -$100
• Shipping: -$0
• Marketing (20% of revenue): -$3,000
• Net profit: $11,375 (75.8% margin)

Highest margins since there's no physical product or shipping. Pure profit after fees and marketing.

The Most Expensive Mistakes Shopify Sellers Make

Mistake #1: Not Using Shopify Payments

The cost: If you use PayPal or Stripe instead of Shopify Payments on a Basic plan:

• You pay 2.9% + $0.30 to PayPal/Stripe
• PLUS 2% additional transaction fee to Shopify
• Total: 4.9% + $0.30 instead of 2.9% + $0.30

On $50,000 monthly revenue, that's an extra $1,000/month ($12,000/year).

The fix: Use Shopify Payments unless you have a very specific reason not to.

Mistake #2: Paying for Unused Apps

The cost: Many stores have 5-10 apps they installed, used once, and forgot about.

• $15/month per unused app × 5 apps = $75/month
• $900/year wasted

The fix: Audit your apps monthly. If you haven't used it in 30 days, cancel it.

Mistake #3: Wrong Shopify Plan

Too low (Basic when you should be on Shopify):

• Processing $100,000/month on Basic plan
• Paying 2.9% + $0.30 = $3,200 in fees
• If you upgraded to Shopify plan ($105/month):
• Paying 2.7% + $0.30 = $3,000 in fees
• Net savings after plan cost: $134/month

Too high (Advanced when you should be on Shopify):

• Processing $20,000/month on Advanced plan ($399/month)
• You're paying $294/month more for minimal savings on transaction fees
• Better to stay on Shopify plan and save $3,500/year

The fix: Calculate break-even points:

• Basic → Shopify: Makes sense at $32,500+/month in sales
• Shopify → Advanced: Makes sense at $197,500+/month in sales

Mistake #4: Not Tracking Product-Level Profitability

The problem: You might be making great margins on Product A, but losing money on Product B - and not know it.

Example:

• Product A: $50 revenue, $15 cost, $10 shipping, $8 ads = $17 profit (34% margin)
• Product B: $30 revenue, $18 cost, $8 shipping, $12 ads = -$8 loss (-27% margin)

If you're selling equal amounts, your blended margin looks okay, but half your products are unprofitable.

The fix: Track profitability by SKU. Cut or reprice products that don't hit your target margin.

Mistake #5: "Free Shipping" That Kills Margins

The trap: You offer free shipping to compete with Amazon. But it costs $6 to ship a $30 product.

The math:

• Sale price: $30
• Product cost: $12
• Shipping: $6
• Fees (3.5%): $1.05
• Marketing (25%): $7.50
• Profit: $3.45 (11.5% margin)

If shipping increases to $8 (happens seasonally), you're down to 5% margin.

The fix:

• Increase product prices to cover shipping
• Set free shipping threshold ($50+)
• Charge for expedited shipping
• Build shipping into product cost upfront

Tools for Tracking Shopify Profit

Built-in Shopify Analytics (Limited)

What it shows:

• Total sales
• Orders
• Average order value
• Top products

What it doesn't show:

• Profit after all fees
• Product-level profitability
• Marketing ROI
• True margins

Cost: Free (included)

Best for: Very basic overview only

Shopify Apps (BeProfit, TrueProfit)

What they do:

• Connect to Shopify
• Track COGS, shipping, fees
• Product-level profitability
• Break-even analysis

Cost: $0-50/month

Pros:

• Built specifically for Shopify
• Easy installation
• Shopify-native interface

Cons:

• Only works for Shopify
• Doesn't track other revenue sources
• Limited if you use multiple platforms

Best for: Shopify-only stores

Multi-Platform Profit Trackers (ProfitClear)

What they do:

• Track profit across Shopify + Stripe + PayPal + Gumroad
• Consolidate all revenue sources
• Automatic fee calculation
• Real-time profit dashboard

Cost: $19-29/month

Pros:

• Works across multiple platforms
• Tracks payment processor fees automatically
• See total business profit in one place
• Not locked to Shopify

Cons:

• Separate tool from Shopify
• Requires connecting multiple accounts

Best for: Sellers using Shopify + other platforms, or planning to expand beyond Shopify

Spreadsheets (Manual Tracking)

What you do:

• Export Shopify data
• Manually enter COGS, fees, expenses
• Calculate profit yourself

Cost: Free (time cost)

Pros:

• Complete control
• Customizable
• No monthly fee

Cons:

• Time-consuming
• Error-prone
• Doesn't scale
• Easy to give up on

Best for: Very early stage (under $5K/month) or people who love spreadsheets

How to Improve Your Shopify Profit Margins

Strategy 1: Increase Average Order Value

Current: $50 average order Goal: $75 average order

How:

• Bundle products together
• Add upsells at checkout
• Offer volume discounts
• Create product tiers (good/better/best)

Impact on profit: If your margin is 30%, a $25 increase in AOV = $7.50 more profit per order. On 500 orders/month = $3,750 additional profit

Strategy 2: Negotiate Product Costs

Once you're doing consistent volume:

• Contact suppliers for bulk discounts
• Order larger quantities
• Find alternative suppliers
• Consider white-labeling

Example: Reduce product cost from $20 to $17 (15% reduction) On 500 units/month = $1,500 monthly savings ($18,000/year)

Strategy 3: Optimize Marketing Spend

The problem: You're spending $15 to acquire a customer who brings $40 in profit

The goal: Spend $10 to acquire that same customer

How:

• Track ROAS (Return on Ad Spend) by campaign
• Cut underperforming ads
• Focus on organic traffic (SEO, social)
• Build email list for repeat customers (free marketing)

Impact: Reduce marketing from 25% to 20% of revenue on $50K/month:

• Before: $12,500 marketing spend
• After: $10,000 marketing spend
• Savings: $2,500/month ($30,000/year)

Strategy 4: Increase Prices

The fear: "Customers will leave!"

The reality: Most Shopify stores are underpriced. A 10% price increase typically only loses 3-5% of customers.

Example:

• Current price: $50 with 500 sales/month = $25,000 revenue
• New price: $55 with 475 sales/month = $26,125 revenue
• Net result: More revenue with fewer orders (lower fulfillment costs)

Plus higher margins since costs didn't change.

Strategy 5: Reduce Refunds

Refunds cost you:

• Lost product
• Lost shipping cost
• Lost marketing cost to acquire customer
• Return shipping (sometimes)
• Processing fees (you don't get these back)

How to reduce:

• Better product photos and descriptions
• Size guides and measurements
• Customer reviews and Q&A
• Clear shipping expectations
• Quality control

A 2% reduction in refund rate on $50K revenue = $1,000 saved monthly

When Your Shopify Store Is Actually Profitable

Revenue doesn't equal profit. Here's how to know if your store is truly profitable:

Healthy Profit Margins by Business Model:

• Dropshipping: 15-20% (minimum acceptable: 10%)
• Print-on-demand: 25-35% (minimum acceptable: 20%)
• Wholesale/Retail: 40-50% (minimum acceptable: 35%)
• Digital products: 70-90% (minimum acceptable: 60%)

Break-Even Analysis:

Calculate your monthly fixed costs:

• Shopify subscription: $39-399
• Apps: $150-500
• Tools/software: $50-200
• Total fixed costs: $250-1,100/month

You need to earn at least this much in profit just to break even.

Example:

• Fixed costs: $500/month
• Average profit per order: $15
• Break-even point: 34 orders/month

Anything below 34 orders, you're losing money.

Cash Flow vs Profit:

Profit = Revenue - All Expenses (shown in reports)

Cash flow = Actual money in your bank account (what you can spend)

The gap:

• You might be "profitable" on paper
• But cash is tied up in inventory
• Or waiting for payment processor transfers
• Or customers used payment plans

Always track both profit AND cash flow.

The Bottom Line on Shopify Profit

Your Shopify dashboard shows revenue, not profit. To know your real margins, you need to account for:

✅ Shopify subscription fees ✅ Payment processing fees (2.5-2.9% + $0.30) ✅ Transaction fees (if not using Shopify Payments) ✅ App subscriptions ✅ Product costs (COGS) ✅ Shipping costs ✅ Marketing spend ✅ Refunds and returns

Most Shopify stores operate on 20-40% profit margins. If yours are lower, something needs to change: pricing, costs, marketing efficiency, or business model.

Track your profit weekly, not just at tax time. Make decisions based on profit, not revenue.

Because at the end of the day, revenue is a vanity metric. Profit pays your bills.

---

Tired of manually calculating Shopify profit? ProfitClear automatically tracks your earnings across Shopify, Stripe, PayPal, and Gumroad. See your real profit in 5 minutes. Try it free for 14 days →