Choosing a Shopify ERP integration is one of the most consequential technology decisions a mid-market retailer or wholesaler makes. Get it right and your ecommerce operation runs on real business data. Get it wrong and you’re back to spreadsheets, manual entry, and systems that don’t talk to each other.

Here’s what to evaluate when choosing a connector.

1. What depth of integration do you actually need?

There’s a spectrum from basic accounting sync to full ERP integration.

Accounting sync (Amaka, MySync): Pushes summarised sales data from Shopify into your accounting system as invoices. Good for bookkeeping. Doesn’t handle product data, pricing rules, inventory by location, or customer-specific pricing.

ERP integration (InSyncer, native ERP connectors, custom builds): Full bidirectional sync of products, pricing, inventory, customers, and orders between your ERP and Shopify. Your ERP stays the source of truth. Shopify reflects your real business data.

Most businesses that run a proper ERP need the full integration, not just accounting sync. If your ERP manages your pricing, inventory, and customer relationships, you want those flowing into Shopify automatically.

2. Is it self-serve or supported?

Self-serve connectors are cheaper upfront but require you to configure entity mappings, troubleshoot sync issues, and maintain the integration yourself. This works if you have strong technical resources in-house.

Supported integrations come with a team that scopes, configures, tests, and maintains the integration. This costs more upfront but reduces risk and time to value. It also means you have people to call when something goes wrong at 2am before a big sale.

The question is: do you want to build integration expertise in-house, or do you want to buy it?

3. How does it handle B2B?

If you sell to trade customers with negotiated pricing, this is the most important question. Most Shopify ERP connectors were built for B2C retail. B2B is an afterthought, or not supported at all.

For B2B on Shopify Plus, you need the connector to sync:

• Customer-specific pricing from your ERP’s price classes or price lists
• Quantity break pricing (volume discounts)
• Promotional pricing with date ranges
• Trade catalogues (which products each customer can see)
• Customer account mapping (linking Shopify companies to ERP debtor accounts)

If your connector can’t do these things, your B2B customers will see generic pricing instead of their negotiated rates, which defeats the purpose of a trade portal.

4. How is it deployed?

Ask about the implementation process:

• How long does it typically take?
• Who configures the integration?
• How is it tested before go-live?
• What happens if your ERP is set up in a non-standard way?
• Who coordinates with your ERP consultant?

A good integration partner will scope your project individually, not give you a generic setup wizard. Every business runs its ERP differently, and the integration needs to match your specific configuration.

5. What happens after go-live?

Go-live is when the real work starts. Edge cases appear. Business rules change. New payment providers get added. Products get restructured.

Ask:

• Who supports the integration after launch?
• Is it a help desk or the same people who set it up?
• How are changes handled when your business evolves?
• What monitoring is in place for sync failures?

6. Questions to ask any integration provider

• How many live integrations do you have with my specific ERP?
• Can you show me case studies from businesses similar to mine?
• What happens if the sync fails on a Friday night?
• Do you work alongside my ERP consultant or replace them?
• What’s the total cost of ownership including implementation and monthly fees?
• Can I talk to an existing client?

Our perspective

We built InSyncer because we saw businesses struggling with exactly these decisions. After 10+ years connecting MYOB systems to Shopify, our position is clear: a supported, purpose-built integration is almost always the better choice for mid-market businesses. The upfront cost pays for itself in faster deployment, fewer errors, and ongoing peace of mind.

That said, if your requirements are simple and you have strong technical resources, a self-serve option might work. The key is being honest about what you actually need — both now and in 12 months.