QuickBooks Online vs Desktop
Key differences in setup and integration for QBO vs QuickBooks Desktop with Shopify.
QuickBooks Online (QBO) and QuickBooks Desktop handle Shopify integrations differently. Here’s what changes based on your platform.
Platform differences
QuickBooks Online (QBO)
- Cloud-based, accessible anywhere
- Real-time API integrations
- Automatic updates
- Built for modern ecommerce workflows
QuickBooks Desktop
- Installed software (Windows/Mac)
- Requires sync windows or manual updates
- More features for complex inventory/manufacturing
- Better for legacy workflows
Integration method impacts
Manual CSV
QBO:
- Use File → Import Data → Import CSV
- Web-based import wizard
- Cleaner for cloud workflows
Desktop:
- Use File → Utilities → Import → Excel Files
- IIF files for more complex imports
- More control over transaction types
No-code connectors (Zapier)
QBO:
- Native OAuth connections (easy setup)
- Real-time API access
- Works from anywhere
Desktop:
- Requires Web Connector or third-party middleware
- Sync happens in batches (not real-time)
- Must keep desktop app running for sync
Accounting-grade apps
QBO:
- Direct API connection via OAuth
- Real-time or scheduled posting
- No additional software needed
Desktop:
- Uses QuickBooks Web Connector
- Requires desktop app to be open during sync
- Sync windows (e.g., hourly, daily)
- Some apps support Desktop Enterprise with hosted access
Feature comparison for Shopify integration
| Feature | QuickBooks Online | QuickBooks Desktop |
|---|---|---|
| Real-time posting | ✓ Yes | △ Via Web Connector only |
| Cloud access | ✓ Yes | ✕ No (unless hosted) |
| Inventory assembly | ✕ No | ✓ Yes |
| Multi-location inventory | ✓ Advanced/Plus | ✓ Premier/Enterprise |
| Job costing | Limited | ✓ Full featured |
| User count | Limited by plan | Up to 40 (Enterprise) |
| Audit log | ✓ Good | ✓ Excellent |
App compatibility
Webgility:
- Supports both QBO and Desktop
- Desktop requires Web Connector
- QBO is real-time, Desktop syncs in batches
A2X:
- Primarily built for QBO
- Limited Desktop support
Most integration apps:
- Prefer QBO (easier API access)
- Desktop support often requires extra setup
Migration considerations
Moving from Desktop to QBO:
- Export Desktop company file
- Use Intuit’s migration tool (free)
- Reconfigure integration app for QBO
- Map accounts (chart of accounts may differ)
- Test posting before going live
Moving from QBO to Desktop:
- Less common, harder to do
- Usually requires accountant assistance
- Integration apps need reconfiguration
Which should you use?
Choose QuickBooks Online if:
- You’re starting fresh or have a simple setup
- You want real-time integration
- You work from multiple locations/devices
- You prefer cloud-based workflows
- Your accountant uses QBO
Choose QuickBooks Desktop if:
- You need advanced inventory features (assembly, job costing)
- You have complex manufacturing workflows
- You’re already on Desktop with clean historical data
- You need more than 25 users (Enterprise)
- Your accountant specializes in Desktop
Setup differences
QBO setup:
- Sign in to QuickBooks Online
- Authorize integration app via OAuth
- Configure account mappings
- Start real-time sync
Desktop setup:
- Install QuickBooks Desktop
- Install Web Connector (if using integration app)
- Download connection file from app
- Configure sync schedule
- Keep QuickBooks open during sync windows
Bottom line
For most Shopify sellers, QuickBooks Online is simpler for integration. Real-time posting, cloud access, and easier app setup make it the better choice.
Choose Desktop only if you have specific needs (advanced inventory, job costing, manufacturing) that require its features.