Shopify Bookkeeping Without Recording Every Sale

The Problem Every Platform Seller Faces

You're running a micro-shop on Shopify, selling apps through the App Store, or processing payments via Stripe. Every month, hundreds of transactions hit your account—but your bank statement shows just one or two payouts.

Recording each individual sale feels overwhelming. You're not alone: 50% of small businesses fail within five years, often because of poor financial management. But here's the good news: if you're a Swiss sole proprietor with revenue under CHF 500,000, you don't need to track every transaction.

Swiss law allows simplified cash-basis accounting—meaning you record income when money hits your bank account, not when customers click "Buy." This guide shows you exactly how to stay compliant while cutting your bookkeeping workload by 90%.

Who Can Use Simplified Accounting in Switzerland?

Eligibility Requirements

You qualify for Einnahmen-Überschussrechnung (EÜR)—Switzerland's simplified accounting method—if you meet these criteria:

✅ Operating as a sole proprietor or partnership (not AG or GmbH)
✅ Annual revenue under CHF 500,000 in the preceding year
✅ Non-corporate legal structure

This applies to most freelancers, indie developers, digital creators, and micro e-commerce sellers. Once you cross CHF 500,000, you'll need to switch to full double-entry bookkeeping under Swiss Code of Obligations (Art. 957 et seq.).

Cash vs. Accrual: What's the Difference?

Cash-basis accounting (EÜR):

• Income recorded when money is received
• Expenses recorded when paid
• No accruals, deferrals, or complex adjustments
• Perfect for platform payouts

Accrual accounting:

• Income recorded when earned (invoice date)
• Expenses recorded when incurred
• Required for inventory-heavy businesses and companies over CHF 500K

For platform sellers receiving net payouts, cash-basis is simpler and legally compliant.

Record Retention Requirements

Swiss law requires you to retain all business documents for 10 years, including:

• Platform monthly reports (App Store Connect, Stripe, Shopify)
• Bank statements
• Payout reconciliation CSVs
• Tax returns and VAT filings

Understanding Shopify's Payout Schedule

When you sell through Shopify Payments, here's what happens:

• Capture period: Shopify holds funds for 3 business days after a customer purchase
• Payout frequency: Daily, weekly, or monthly (your choice)
• Minimum threshold: CHF 5 or EUR 1
• Currency options: CHF, EUR, or multi-currency accounts

Example timeline:

Recording Shopify Payouts

Wait for each net payout to appear in your bank account, then make one entry:

2025-07-04  Bank (Shopify Payments)   CHF 10,000
                Sales – Shopify            CHF 10,000

What this number includes:

• Gross sales revenue
• Minus Shopify subscription fee (Basic: CHF 39/month, Shopify: CHF 105/month)
• Minus payment gateway fees (1.9-2.7% + CHF 0.30 per transaction for Swiss cards)
• Minus refunds and chargebacks (automatically netted)

You don't need to break these down individually. The net payout represents your actual income.

Handling Multiple Payouts Per Week

If Shopify deposits funds multiple times per week, you have two options:

Daily recording:

2025-07-04  Bank          CHF 1,500 → Sales – Shopify
2025-07-11  Bank          CHF 2,200 → Sales – Shopify
2025-07-18  Bank          CHF 1,800 → Sales – Shopify

Monthly summary:

2025-07-31  Bank          CHF 5,500 → Sales – Shopify (July total)

Both are compliant. Choose monthly if you want fewer entries; daily if you prefer matching bank statement dates exactly.

Multi-Currency Sales

If you receive payouts in EUR or USD:

1. Record the actual CHF amount deposited in your Swiss bank account
2. Let your bank's exchange rate determine the converted value
3. No need to track original sale currencies individually

Example:

• Shopify sends EUR 1,500
• Your bank converts at 1.047 and deposits CHF 1,570
• Record: CHF 1,570 → Sales – Shopify

Stripe Accounting for Swiss Businesses

Stripe Fee Structure (2026 Rates)

Stripe charges different fees based on card origin:

Stripe Payout Timing

• Default schedule: Daily payouts (if volume exceeds threshold), otherwise weekly
• Processing time: 2 business days after transaction
• Availability: Payouts calculated at 12:00 AM daily, available in reports by 12:00 PM next day

Recording Stripe Income

Each month, summarize your total net payouts:

2025-07-28  Bank (Stripe CH)      CHF 5,000
                Sales – Stripe         CHF 5,000

This represents:

• Gross card payments received
• Minus all Stripe processing fees
• Minus refunds and disputes
• = Net cash deposited

Pro tip: Download Stripe's Payout Reconciliation Report monthly. While not required for each entry, it provides backup documentation for tax audits.

Handling Refunds and Chargebacks

Don't record these separately. Stripe automatically deducts refunds from your next payout. Your net deposit already reflects the adjustment.

Example:

• Week 1 sales: CHF 3,000 (gross)
• Week 2 refund: -CHF 200
• Week 2 sales: CHF 2,500 (gross)
• Net payout: CHF 5,300 (after fees)
• Your entry: CHF 5,300 → Sales – Stripe

Apple App Store & In-App Purchases

How Apple Pays Developers

Apple operates on a monthly payment cycle:

1. Sales period: Full calendar month
2. Commission deduction: 15% (Small Business Programme) or 30% (standard)
3. Payment date: ~45 days after month-end
4. Minimum threshold: Must exceed region-specific minimum (typically USD 250 equivalent)

Small Business Programme: If your proceeds in the previous calendar year were under USD 1 million, you qualify for the reduced 15% commission.

Recording App Store Income

Wait for Apple's monthly wire transfer, then record:

2025-08-15  Bank                     CHF 2,850
                Sales – Apple App Store   CHF 2,850

This single entry covers:

• All app sales
• All in-app purchases
• All subscription renewals
• Minus Apple's 15-30% commission

Accessing Apple Reports

Log into App Store Connect → Payments → Monthly Reports

Download these files for record retention:

• Financial reports (sales by territory)
• Payments and financial reports (net proceeds)
• Tax withholding summaries (if applicable)

Store these PDFs for your 10-year retention requirement.

Case Study 1: Indie App Developer

July 2025 activity:

Accounting entries:

2025-07-31  Bank          CHF 5,200 → Sales – Stripe
2025-08-15  Bank          CHF 3,500 → Sales – Apple

Monthly profit: CHF 8,700 minus operating expenses (hosting, software, home office allocation)

Case Study 2: Shopify Multi-Channel Seller

July 2025 activity:

Accounting entries:

2025-07-07  Bank (Shopify)    CHF 1,570 → Sales – Shopify
2025-07-14  Bank (Shopify)    CHF 2,500 → Sales – Shopify
2025-07-28  Bank (Stripe)     CHF 3,000 → Sales – Stripe

Total July income: CHF 7,070

Cost of goods sold: Tracked separately based on inventory purchases (recorded when paid to suppliers)

End-of-Month Procedures

Follow this process to ensure accuracy:

Week 1:

1. ✅ Export all platform payout reports (Shopify, Stripe, Apple)
2. ✅ Download bank statements showing deposits
3. ✅ Match each payout report total to bank deposit amount

Week 2: 4. ✅ Record each net payout as single line item in accounting software 5. ✅ Categorize by platform (Sales – Shopify, Sales – Stripe, etc.) 6. ✅ File digital copies of all reports in dated folders

Week 3: 7. ✅ Cross-check: Does total recorded income = total bank deposits? 8. ✅ Identify any missing payouts or timing differences 9. ✅ Note any holds, reserves, or delayed payments

Week 4: 10. ✅ Calculate month-to-date revenue by platform 11. ✅ Compare to previous months for anomaly detection 12. ✅ Prepare VAT calculation if applicable (see below)

Common Reconciliation Issues

Problem: Shopify payout report shows CHF 10,200, but bank deposit is CHF 10,000

Cause: Currency conversion, last-minute refund, or split payout

Solution: Record the actual bank deposit amount (CHF 10,000). The difference will appear in next payout or fees.

Problem: Stripe shows daily payouts but you prefer monthly entries

Solution: Sum all July payouts into one entry at month-end. Your bank statement will still show daily deposits, but your accounting shows the monthly total.

Problem: Apple payment didn't arrive 45 days after month-end

Cause: Didn't meet minimum threshold for your region

Solution: Wait for next month. Apple will pay accumulated balance when threshold is reached.

VAT Considerations for Swiss Sellers

When You Need to Register for VAT

How Platform VAT Works

Good news: Shopify, Stripe, and Apple handle most VAT complexity for you.

Shopify: Automatically calculates Swiss VAT at checkout based on customer location. Your payout already reflects VAT collected.

Recording method:

Bank Account                 CHF 10,000
    Sales – Shopify (net)        CHF 9,251
    VAT Payable (8.1%)             CHF 749

Stripe: You configure VAT rules in Dashboard → Settings → Tax settings. Stripe adds VAT to invoices but doesn't automatically split it in payouts.

Apple: For Swiss customers, Apple adds VAT and remits it directly to Swiss tax authorities under the One-Stop Shop (OSS) system. You typically don't handle this.

Quarterly VAT Filing

If registered, you must file VAT returns quarterly:

1. Sum all Sales – Shopify and Sales – Stripe entries
2. Calculate 8.1% output VAT on net sales
3. Deduct input VAT from business purchases
4. Pay difference to Swiss Federal Tax Administration

Deadlines: 60 days after quarter-end (Jan 31, Apr 30, Jul 31, Oct 31)

Automation Saves 120+ Hours Annually

Manual bookkeeping for platform sales is tedious:

• Downloading 12 monthly reports per platform = 36 reports/year
• Matching each to bank statements = ~2 hours/month
• Data entry = ~3 hours/month
• Total: 60 hours/year minimum

With automation (like Magic Heidi):

• Platform connections sync payouts automatically
• Bank feeds match deposits instantly
• VAT calculations happen in real-time
• Time saved: 50+ hours/year (that's 25% of your admin workload)

What to Look for in Software

✅ Swiss legal compliance: Supports CHF 500K threshold, EÜR method
✅ Multi-platform connections: Shopify + Stripe + Apple in one place
✅ Multi-currency handling: Converts EUR/USD payouts to CHF automatically
✅ VAT automation: Calculates 8.1% and generates quarterly reports
✅ Bank feed integration: Matches payouts to bank deposits
✅ Multi-language: German, French, Italian, English support

Growth Path

You now know how to legally record platform payouts without tracking every transaction. This simplified method:

✅ Saves 50+ hours annually compared to manual transaction entry
✅ Maintains full Swiss legal compliance under CHF 500K threshold
✅ Reduces error risk from 5% to under 1% with automation
✅ Works across platforms – Shopify, Stripe, Apple, and others

Your Next Steps

1. Export this month's platform reports (Shopify, Stripe, Apple)
2. Open your bank statement and match payout deposits
3. Record net payouts as single entries per platform
4. Store reports in dated folders for 10-year retention

Want to automate the entire process? Magic Heidi connects directly to your platforms and bank, recording payouts automatically while maintaining Swiss compliance.

Try Magic Heidi free for 30 days → No credit card required. Full multi-platform support. Swiss-specific accounting rules built in.

Questions? Contact our Swiss accounting specialists at support@magicheidi.com or explore our complete feature list for freelancers and sole proprietors.