What This Guide Covers
This guide walks you through everything you need to know about using Synder with Shopify and QuickBooks Online (QBO). 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.
💡 Tip: Don’t sync anything yet! Configure your settings first (see Essential Settings below).
Understanding Synder Sync Modes
This is one of the most important decisions you’ll make. Synder offers two main ways to record your Shopify sales in QBO:
Per-Transaction Sync
What it does: Creates one entry in QBO for every individual sale.
Best for:
- Stores with fewer than ~50 transactions per day
- Sellers who want to see every order in their books
- Businesses that need to match specific orders to specific customers
What gets created in QBO:
- 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:
- Stores with 50+ transactions per day
- Sellers who want clean, simple books
- Businesses that don’t need individual order detail in QBO
Pros: Clean books. Fewer entries. Faster reconciliation.
Cons: Can’t trace individual orders in QBO.
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 Your Sync Mode
- Under 50 orders/day, want full detail → Per Transaction
- Over 50 orders/day, want simplicity → 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 for Shopify Bookkeeping Automation
Before you sync your first transaction, configure these settings. This takes about 5 minutes and prevents 90% of common errors.
Navigate to: Settings → Shopify
Setting 1: Income Account
What it does: Tells Synder where to record your sales revenue in QBO.
Where: Settings → Shopify → Mapping → Income Account
Recommended: “Sales of Product Income” (QBO default) — or create a dedicated “Shopify Sales” account if you want to track Shopify revenue separately.
⚠️ If this is left blank or mapped incorrectly, your sales will land in “Uncategorized Income.”
Setting 2: Clearing (Bank) Account
What it does: Acts as a staging area for money between Shopify and your bank account — a virtual “in transit” account.
Where: Settings → Shopify → Mapping → Bank Account / Clearing Account
Options:
- Undeposited Funds — QBO’s built-in clearing account (simplest option)
- A dedicated clearing account — e.g., “Shopify Clearing” (better for tracking)
Why this matters: If the clearing account is wrong, your bank reconciliation won’t balance.
Setting 3: Tax Mapping
Where: Settings → Shopify → Mapping → Tax Mapping
- Synder shows tax names from Shopify (e.g., “State Tax 8.5%”)
- Match each to the corresponding QBO tax rate
- If no matching tax exists in QBO, create one first, then return to map it
💡 If you don’t collect sales tax, you can skip this. But if you do collect tax and skip this setting, expect sync errors.
Setting 4: Product/Service Mapping
Where: Settings → Shopify → Mapping → Products
This controls how your Shopify products appear in QBO. See the Product Mapping section below.
Bonus Settings Worth Checking
- 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 & Inventory Mapping
Basic Product Mapping
When Synder encounters a Shopify product it hasn’t seen before, it can either:
- Create a new product in QBO automatically, or
- Map it to an existing product in QBO
Options:
- Auto-create products — Synder creates matching products in QBO 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 QBO product/service. Most control, but more setup work.
Inventory Tracking (COGS & 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 QBO/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 QBO
Important limitations:
- Synder updates QBO inventory based on sales and refunds only
- Manual inventory adjustments in Shopify are NOT synced
- Inventory sync goes one way: Shopify → QBO (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 & 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 QBO 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 & 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 QBO: Each order should appear as a Sales Receipt or Invoice + Payment
- Match payouts to bank deposits: In QBO, 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 QBO
Troubleshooting Common Synder 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 QBO”
Cause: Shopify’s native QBO integration running alongside Synder.
Fix: Disable Shopify’s built-in QuickBooks integration. Use only Synder.
Quick Reference: First-Time Synder Shopify Setup
- ✅ Connect Shopify to Synder
- ✅ Connect ALL other payment gateways (PayPal, Stripe, etc.)
- ✅ Set Sync Mode (Per Transaction or Summary)
- ✅ Map Income Account
- ✅ Map Clearing/Bank Account
- ✅ Map Tax rates
- ✅ Configure Product mapping
- ✅ Enable Manual/POS/Other orders if applicable
- ✅ Verify time zone matches Shopify
- ✅ Sync a few test transactions and verify in QBO
Need More Help?
- Synder Help Center: synder.com/help — searchable articles and guides
- Email Support: [email protected] — typically responds within 24 hours
- In-App Chat: Click the chat bubble in the bottom-right corner of Synder
This guide is maintained by the Synder team. For the latest updates, visit synder.com/help.
