Step-by-step guide to connecting Shopify to Synder. Learn sync modes, essential settings, product mapping, and troubleshooting for automated e-commerce bookkeeping.
What This Guide Covers
This guide walks you through everything you need to know about using Synder with Shopify and QuickBooks Online. It’s written for solo Shopify sellers who handle their own bookkeeping — no accounting degree required.
By the end, you’ll know how to:
- Connect Shopify to Synder correctly
- Choose the right sync mode for your business
- Configure settings so transactions land in the right accounts
- Map your products for accurate revenue tracking
- Reconcile your books with confidence
- Fix the most common issues yourself
Time to set up: About 15–20 minutes for initial configuration.
Before You Start: Prerequisites
Make sure you have these ready:
- A Shopify store with at least a few orders processed
- A QuickBooks Online account (any plan)
- A Synder account — sign up at synder.com if you don’t have one
- All payment gateways identified — know how your customers pay (Shopify Payments, Stripe, PayPal, etc.)
Critical Rule: Connect ALL Your Payment Gateways
This is the #1 mistake new users make. If your Shopify store accepts payments through Shopify Payments and PayPal and Stripe, you must connect all three to Synder.
Why? Synder pulls order details (items, tax, shipping) from Shopify, but it pulls fee and payout data from each payment gateway. If a gateway isn’t connected, those transactions will be incomplete or missing entirely.
Connecting Shopify to Synder
Step-by-Step Connection
Step 1: Start the connection
- Log into Synder at go.synder.com
- If you’re new: the onboarding wizard will prompt you to connect a platform
- If you’re adding Shopify to an existing organization: go to Settings → Integrations → + Add Integration
Step 2: Select Shopify
- Find Shopify in the platform list and click Connect
- You’ll be redirected to Shopify’s authorization page
Step 3: Authorize the connection
- Log into your Shopify account if prompted
- Important: If you have multiple Shopify stores, double-check you’re connecting the correct one
- Click Install App to grant Synder access
Step 4: Verify the connection
- Back in Synder, you should see Shopify listed under your integrations
- Shopify Payments (if you use it) will automatically connect alongside your Shopify store
Step 5: Connect additional payment gateways
- If you also accept PayPal, Stripe, or other gateways, connect each one separately through Settings → Integrations
What Happens After Connection
Synder will begin pulling your historical data. Depending on your order volume, this can take a few minutes to several hours. You’ll see transactions appear in the Transactions tab with a “Ready to sync” status.
Important: Don’t sync anything yet! Choose your sync mode and configure your settings first.
Choosing Your Sync Mode
This is one of the most important decisions you’ll make. Synder offers two main ways to record your Shopify sales in QuickBooks Online. The right choice depends on how much detail you need and how many orders you process.
Per-Transaction Sync
What it does: Creates one entry in QuickBooks Online for every individual sale.
Best for:
- Businesses that need granular, per-order detail in their books
- Sellers who need to match specific orders to specific customers
- Stores with moderate transaction volume (under ~50/day)
What gets created in QuickBooks Online:
- Customer order → Sales Receipt or Invoice + Payment
- Refund → Refund Receipt
- Payout → Transfer (clearing → bank)
- Fee → Expense
Pros: Full visibility into every transaction. Easy to trace any order.
Cons: Can clutter your books if you have high volume.
Daily Summary Sync
What it does: Rolls up all transactions for a day (or per payout) into a single Journal Entry.
Best for:
- Businesses that prioritize clean, simple books over per-order detail
- High-volume stores (50+ transactions per day)
- Sellers who don’t need to trace individual orders in QuickBooks Online
Pros: Clean books. Fewer entries. Faster reconciliation.
Cons: Can’t trace individual orders in QuickBooks Online.
Per-Payout Summary (Shopify Payments only)
If you use Shopify Payments, you can also choose Per-Payout Summary, which groups transactions by payout cycle instead of calendar day. This makes reconciliation easier since each summary maps to one bank deposit.
How to Choose
- Need per-order detail, moderate volume → Per Transaction
- Want simplicity, high volume → Daily Summary
- Use Shopify Payments, want easy bank matching → Per-Payout Summary
- Not sure yet → Start with Per Transaction — you can switch later
Where to set it: Settings → Shopify → General → Sync Mode
Essential Settings
Before you sync your first transaction, configure these settings. This takes about 5 minutes and prevents 90% of common errors.
Navigate to: Settings → Shopify
For detailed configuration instructions for each setting (income account, clearing account, fees, product mapping, and taxes), see Configure Synder Before Your First Sync. That guide covers every setting in depth.
Here are the Shopify-specific settings to pay attention to:
Shopify-Specific Settings
- Time Zone (Settings → Shopify → General) — Match this to your Shopify time zone to avoid date mismatches
- Manual Orders (Settings → Shopify → General) — Enable to sync orders paid outside Shopify
- POS Orders (Settings → Shopify → General) — Enable to sync in-person sales from Shopify POS
- Other Orders (Settings → Shopify → General) — Enable to sync orders from unsupported payment gateways
Product and Inventory Mapping
Basic Product Mapping
When Synder encounters a Shopify product it hasn’t seen before, it can either:
- Create a new product in QuickBooks Online automatically, or
- Map it to an existing product in QuickBooks Online
Options:
- Auto-create products — Synder creates matching products in QuickBooks Online using the Shopify product name and SKU. Best for stores with many products.
- Use a generic product — All sales map to a single “Shopify Sale” product. Simplest, but less granular.
- Manual mapping — You map each Shopify product to a specific QuickBooks Online product/service. Most control, but more setup work.
Inventory Tracking (COGS and Quantity)
Synder supports inventory tracking:
- Quantity on Hand: Updates automatically when orders are synced. Important: This is one-way only (Shopify → accounting software). Inventory changes made directly in QuickBooks Online/Xero will not sync back to Shopify, and manual Shopify adjustments are not reflected in your books.
- Cost of Goods Sold (COGS): Tracked if inventory items are set up in QuickBooks Online.
Important limitations:
- Synder updates QuickBooks Online inventory based on sales and refunds only
- Manual inventory adjustments in Shopify are NOT synced
- Inventory sync goes one way: Shopify → QuickBooks Online (not back)
- Bundles and assemblies are available on Large plans only
Tip: Set up your products and inventory before syncing historical transactions to prevent quantity mismatches.
How Synder Handles Shopify Transactions
Sales
- Standard order (Shopify Payments) → Sales Receipt or Invoice + Payment (includes items, tax, shipping, discounts)
- Manual order → Sales Receipt or Invoice + Payment (goes to Manual Orders clearing account)
- POS order → Sales Receipt or Invoice + Payment (goes to POS Orders clearing account)
Refunds
- Full refund → Refund Receipt (reverses the original sale)
- Partial refund (items) → Refund Receipt (only the refunded items/amounts)
- Partial refund (amount) → Refund Receipt (dollar amount without specific items)
Payouts and Fees
- Payout → Transfer (from clearing account to your bank)
- Processing fee → Expense (Shopify’s payment processing fees)
- Chargeback/dispute → Expense (disputed amount + chargeback fee)
- Shipping label → Expense (cost of Shopify shipping labels)
When Do Transactions Sync?
Critical to understand: Synder syncs Shopify transactions only after the payout occurs. If you just made a sale today, it won’t appear in Synder until Shopify processes the payout (usually 1–3 business days).
This is the #1 reason users think transactions are “missing.”
Special Order Types
Manual Orders
Orders where the customer pays outside of Shopify (cash, check, bank transfer).
- Must enable Manual Orders in settings
- Sync to a dedicated “Shopify Manual Orders” clearing account
- Not included in Shopify payouts — you must manually reconcile these
Reconciliation: Confirm you received the external payment → manually create a Transfer in QuickBooks Online from the Manual Orders clearing account to your bank account.
POS Orders
- Must enable POS Orders in settings
- Sync to a dedicated “Shopify POS Orders” clearing account
Other Orders
Orders paid through unsupported gateways (e.g., Klarna, Afterpay).
- Must enable Other Orders in settings
- Shopify doesn’t provide fee or payout data for these gateways
- Reconcile using the external gateway’s own reports
Gift Cards and Discounts
Gift Cards
Gift card purchased as a product: Synced like a normal sale.
Gift card used as payment: The gift card portion reduces the order total. Only the remaining balance flows through the payment gateway.
Known quirk: Gift cards are synced as line items. You may see discrepancies when reconciling against Shopify’s “Net payments by order” report. Filter them out using the “Payment gateway” column.
Discounts
- Coupon/discount code discounts — recorded with the discount name
- Automatic discounts — recorded as applied
- Line-item discounts — applied to the specific product line
Shop Cash (Shopify Balance Rewards)
If your customers use Shop Cash (rewards earned through Shopify’s Shop app), be aware that these transactions require special handling:
- Shop Cash is a separate payment method — it does not flow through Shopify Payments or your other gateways. If you don’t configure it, these transactions may appear as “missing.”
- Setup: In Synder, go to Settings → Shopify → “Create Additional Settings” → add Shop Cash as a payment method.
- Reconciliation impact: Shop Cash payouts arrive on a different schedule than Shopify Payments. Track them separately in your clearing accounts.
- Common issue: If Shop Cash transactions are missing from Synder, it’s almost always because the additional payment method wasn’t configured. This is not a bug — it’s a setup step.
Reconciliation: Making Your Books Match
Per-Transaction Reconciliation
- Get your Shopify report: Go to Analytics → Reports → “Net payments by order” → Export CSV
- Verify data in QuickBooks Online: Each order should appear as a Sales Receipt or Invoice + Payment
- Match payouts to bank deposits: In QuickBooks Online, go to Banking → For Review
Daily Summary Reconciliation
- Use Shopify’s Finances Summary for the period
- Check that each Daily Summary shows as “Fully Fetched” in Synder
- Match Journal Entry totals with the Finances Summary
Multi-Gateway Reconciliation
If customers pay through multiple gateways:
- Synder creates separate clearing accounts per payment method
- Compare each clearing account only to the matching gateway’s transactions
Monthly Reconciliation Checklist
- All transactions synced (no “Ready to sync” or “Pending” items)
- All Daily Summaries show “Fully Fetched” (if using summary mode)
- Clearing account balances match gateway reports
- Payouts/Transfers match bank deposits
- Refunds are accounted for
- Manual/POS/Other orders are reconciled separately
- No “Uncategorized” transactions in QuickBooks Online
Troubleshooting Common Shopify Issues
“My recent Shopify orders aren’t showing in Synder”
Cause: Synder syncs transactions only after the payout occurs (1–3 business days).
Fix: Wait for the payout. Check status in Shopify under Finance → Payouts.
“Transactions from PayPal/Stripe aren’t syncing”
Cause: That payment gateway isn’t connected to Synder.
Fix: Go to Settings → Integrations and connect the missing gateway.
“Transaction dates don’t match”
Cause: Time zone mismatch.
Fix: Go to Settings → Shopify → General → Time Zone and match your Shopify store’s time zone.
“Sales are going to Uncategorized Income”
Cause: Income account not mapped.
Fix: Go to Settings → Shopify → Mapping → Income Account and select the correct account.
“Bank reconciliation doesn’t balance”
- Verify the clearing account is set correctly
- Check that all payment gateways are connected
- Reconcile Manual/POS/Other orders separately
- Check for multi-currency issues
“Daily Summary shows Partially Fetched”
Fix: Check for pending transactions, run a manual import, and refresh/regroup the summary. If the issue persists, contact Synder support.
“Duplicate transactions in QuickBooks Online”
Cause: Shopify’s native QuickBooks Online integration running alongside Synder.
Fix: Disable Shopify’s built-in QuickBooks integration. Use only Synder to avoid duplicates.
Need Help?
If you’ve followed this guide and are still running into issues, contact the Synder support team. Include screenshots and the Explain details from any failed transactions — it helps the team resolve your issue faster.
Related articles:
- Settings Checklist: Configure Synder Before Your First Sync
- Common Sync Errors and How to Fix Them
- How to Review Your Synced Transactions and Fix Errors
- Per Transaction Sync: Synder User Guide
- How Summary Sync Works: User Guide
