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Shopify Payments First Week Setup

You just launched your Shopify store. Shopify Payments is already enabled. But don't process real orders until you complete this 7-day checklist. These configurations prevent chargebacks, improve conversion, and save money.

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Why This Matters​

Common Shopify first-week mistakes:

  • Using third-party gateway → Pay extra 2% transaction fee unnecessarily
  • Missing shipping confirmations → 40% more "not received" disputes
  • No fraud analysis enabled → First fraud attack drains inventory
  • Wrong refund policy → Customer confusion and disputes
  • No abandoned cart recovery → Lose 10-20% of potential sales

This checklist prevents these. Budget 4-6 hours over 7 days.

Day 1: Payments Configuration (1 hour)​

Task 1: Verify Shopify Payments is Enabled (10 min)​

Where: Shopify Admin → Settings → Payments

Verify:

  • Shopify Payments is activated (not PayPal or Stripe)
  • Status shows "Active"
  • Bank account connected for payouts

Why Shopify Payments:

  • Avoid 2% third-party transaction fee
  • Unified reporting (sales + payments)
  • Faster payouts

If you see "PayPal" or "Stripe": Remove them or you're paying extra 2% on every transaction.

Task 2: Configure Payout Schedule (10 min)​

Where: Settings → Payments → Payout Schedule

Options:

  • Daily (recommended)
  • Weekly
  • Monthly

Choose: Daily for consistent cash flow.

Payout timing: 2-3 business days (standard)

Why it matters: Daily = predictable cash flow. Weekly = lumpy cash flow.

Task 3: Set Fraud Analysis Level (15 min)​

Where: Settings → Payments → Fraud Analysis

Levels:

  • Low: Analyze fewer orders (higher fraud risk)
  • Medium: Default (recommended for most)
  • High: Analyze more orders (lower fraud risk, may hold legitimate orders)

Start with: Medium

Shopify will flag suspicious orders - you decide whether to fulfill.

Why it matters: Level too low = fraud gets through. Level too high = legitimate orders held.

Task 4: Enable 3D Secure (Verify) (10 min)​

Where: Settings → Payments

Verify 3D Secure (SCA) is enabled:

  • Should be ON by default for European cards
  • Required for PSD2 compliance

If selling to EU: 3DS is automatic. No action needed.

If US-only: 3DS will still trigger for high-risk transactions.

Why it matters: European issuers decline non-3DS transactions. You need this enabled.

Task 5: Test Checkout (15 min)​

Before going live:

Use Shopify's test mode:

  1. Enable test mode (Settings → Payments)
  2. Use Shopify test card: 1 (Visa)
  3. Complete full checkout
  4. Verify confirmation email arrives
  5. Check order shows in Orders tab
  6. Disable test mode

Why it matters: Bugs in checkout = lost sales. Test before customers arrive.

Day 2: Fraud and Chargeback Prevention (1.5 hours)​

Task 6: Set Up Fraud Indicators (30 min)​

Where: Orders → Order Details (on flagged orders)

Shopify shows fraud indicators:

  • AVS mismatch (billing address doesn't match)
  • CVV mismatch
  • High-risk country
  • Unusual order patterns

Your job: Decide whether to fulfill or cancel

Best practice - Cancel if:

  • AVS and CVV both fail
  • Customer is new + high-value order + suspicious email
  • Shopify recommends cancellation

Why it matters: One $500 fraud order = 15-20 legitimate orders worth of profit lost.

Task 7: Configure Shipping Confirmations (30 min)​

Where: Settings → Notifications → Shipping

Enable:

  • Shipping confirmation email (to customer)
  • Include tracking number
  • Send when order is fulfilled

Why it matters: Shipping confirmations reduce "not received" disputes by 40-60%. This is the #1 chargeback prevention tool.

Task 8: Set Up Order Confirmation Emails (30 min)​

Where: Settings → Notifications → Orders

Customize order confirmation:

  • Include clear business name
  • Add customer support email
  • Include refund policy link
  • Show item descriptions clearly

Why it matters: Clear confirmations prevent "I didn't order this" disputes.

Day 3: Checkout Optimization (1 hour)​

Task 9: Optimize Checkout Settings (30 min)​

Where: Settings → Checkout

Configure:

  • Customer information: Email required
  • Customer accounts: Optional (don't force signup)
  • Shipping address: Require for physical goods
  • Abandoned checkout recovery: Enable (automatic emails)

Abandoned cart emails:

  • Send 1 hour after abandonment
  • Include cart contents
  • 10-20% of abandoned carts convert

Why it matters: Abandoned cart recovery = 10-20% more sales at $0 cost.

Task 10: Add Trust Signals to Checkout (30 min)​

Where: Theme customization → Checkout

Add:

  • Security badges (SSL, trust seals)
  • Clear refund policy link
  • Customer support contact
  • Estimated delivery time

Why it matters: Trust signals increase conversion 5-15%.

Day 4-5: Refund and Return Policy (1 hour)​

Task 11: Create Clear Refund Policy (30 min)​

Where: Your website + Settings → Policies

Your refund policy must include:

  • Timeframe (30 days, 60 days, etc.)
  • Conditions (unopened, unused, etc.)
  • Process (how to request refund)
  • Timeline (how long for refund to process)

Link to policy:

  • Footer of every page
  • Checkout page
  • Confirmation emails

Why it matters: Clear policy shown at checkout reduces disputes by 15-20%.

Task 12: Configure Shopify Return Settings (30 min)​

Where: Settings → Shipping and Delivery → Returns

Set up:

  • Return window (match your policy)
  • Return shipping cost (customer pays or you pay)
  • Restocking fee (if applicable)

Why it matters: Makes returns easy = fewer chargebacks. Customers prefer to return properly than dispute.

Day 6-7: Monitoring and Optimization (1 hour)​

Task 13: Review First Orders (30 min)​

Check first 10-20 orders:

  1. Fraud indicators: Any flagged?
  2. How you handled flagged orders
  3. Customer emails received?
  4. Any refund requests?
  5. Shipping working properly?

Learn from first customers before scaling.

Task 14: Set Up Weekly Monitoring (30 min)​

Create process:

Every Monday:

  • Review last week's sales (Orders → Export)
  • Check fraud rate (flagged / total)
  • Check refund rate (refunds / total)
  • Review any disputes

Set targets:

  • Fraud rate: Under 1%
  • Refund rate: Under 5-10% (varies by industry)
  • Disputes: 0 in first month

Why it matters: Catching CB ratio spike in Week 2 vs Month 3 saves your account.

Shopify-Specific Gotchas​

1. Third-Party Payment Gateway Fee​

If you use Stripe or PayPal instead of Shopify Payments:

  • Basic plan: +2.0% extra
  • Shopify plan: +1.0% extra
  • Advanced plan: +0.5% extra

On $100K/month with Basic plan:

  • Shopify Payments: $3,200 fees
  • Stripe: $3,200 + $2,000 = $5,200 fees
  • Extra: $2,000/month ($24,000/year)

Never use third-party gateway unless Shopify Payments unavailable in your country.

2. Plan Tier Optimization​

Review pricing by tier:

At $150K/month:

  • Basic ($39): $39 + 2.9% = $4,389/month total
  • Shopify ($105): $105 + 2.7% = $4,155/month total
  • Savings: $234/month by upgrading

Upgrade to Shopify plan if processing >$100K/month. The $66/month upgrade pays for itself.

3. Chargeback Threshold​

Shopify Payments has lower threshold than Stripe:

  • Warning at 0.6-0.65%
  • Risk at 0.75%+
  • Termination possible at 1.0%+

Monitor from Day 1. Shopify is less forgiving than Stripe.

Test to Run​

End of Week 1 audit:

Checklist:

  • Shopify Payments enabled (not third-party)
  • Email receipts working
  • Shipping confirmations configured
  • Fraud analysis set to Medium
  • Refund policy published and linked
  • Abandoned cart recovery enabled
  • Test order completed successfully
  • First 10 orders processed without issues
  • No chargebacks received
  • Monitoring process established

Success criteria: All boxes checked by end of Week 1.

Scale Callouts​

First $10K processed:

  • Monitor every order manually
  • Review all fraud flags
  • Respond to customers within 2 hours

First $100K processed:

  • Consider upgrading to Shopify plan ($105) for lower rates
  • Weekly monitoring sufficient
  • Patterns established

First $500K processed:

  • Evaluate if Advanced plan ($399) worth it
  • Review chargeback ratio (should be under 0.5%)
  • Consider additional fraud tools if needed

Beyond $1M:

  • Calculate if custom platform + Stripe cheaper than Shopify
  • Migration costs are high ($50K-200K)
  • But savings may justify at very high volume

Where This Breaks​

  1. High-risk products: Shopify rejects supplements, CBD-adjacent, adult products faster than other processors. Verify your products are acceptable.

  2. International immediately: If 50%+ sales are international from Day 1, add multi-currency setup to this checklist (extra 2-3 hours).

  3. Subscription products: If selling subscriptions, add subscription app setup (ReCharge, Bold, etc.) - extra 4-6 hours.

  4. Print-on-demand/dropshipping: Long shipping times (2-4 weeks) = higher dispute risk. Extra fraud prevention needed.

  5. Volume spike: If you launch and do $100K in first week, Shopify will hold your account for review. Expect 3-7 day delay.

Next Steps​

Completed first week?

  1. Review Shopify Payments Profile for optimization
  2. Read Operations Checklist for ongoing tasks
  3. Optimize based on first month data

Need to reduce costs?

  1. Calculate which Shopify plan tier optimizes your costs
  2. See Total Cost Model
  3. Review Processor Comparison

Growing and optimizing?

  1. Checkout Conversion - Improve conversion rates
  2. Chargeback Prevention - Reduce disputes
  3. Auth Optimization - Improve approval rates

See Also​