The short answer
Your online store is good at taking orders. Your ERP or accounting system is good at stock, invoicing and the books. Connecting them means deciding, for each type of record, which system owns it, which direction it moves and how quickly. In most setups, orders, customers and payments flow from the store into the ERP, while items, prices and available stock flow from the ERP out to the store. Get that ownership map right and the choice of connector becomes much easier. Skip it and you end up with duplicate customers, oversold stock and a month-end reconciliation nobody enjoys.
What actually needs to flow
Start with a simple table. We fill one in with every client before any tool is chosen.
| Record | Usual owner | Usual direction | How often |
|---|---|---|---|
| Items, SKUs, descriptions | ERP | ERP to store | On change |
| Prices and price lists | ERP | ERP to store | On change |
| Available stock | ERP | ERP to store | Near real time for fast sellers, scheduled for the rest |
| Orders | Store | Store to ERP | Near real time |
| Customers and addresses | Store (new), ERP (billing terms) | Store to ERP | With each order |
| Taxes charged | Store (at checkout) | Store to ERP, as charged | With each order |
| Payments and payouts | Payment processor | Processor to ERP | Daily |
| Refunds and returns | Store or ERP (agree which) | Both ways | On event |
| Fulfilment and tracking | ERP or shipping tool | Back to store | On shipment |
Two rules save most of the pain. First, every item needs one shared identifier (usually the SKU) in both systems. Second, the ERP should record the tax the customer was actually charged, not recalculate it.
Three ways to connect
1. A ready-made connector. Many ERPs and accounting packages offer connectors for popular store platforms. ERPNext, for example, has a Shopify connector (now delivered through a separate ecommerce integrations app) that creates sales orders from Shopify orders and pushes stock levels from mapped warehouses back to Shopify on an hourly schedule (ERPNext documentation). Its WooCommerce integration is simpler, one-way from store to ERP, and is marked as deprecated in version 15 (ERPNext documentation). Connectors are the fastest start, but check exactly what they sync, how often, and who maintains them.
2. An integration platform. A subscription integration service sits between the systems and lets you configure flows with less code. It handles more variations than a fixed connector, at the cost of another subscription (often priced in US dollars) and another place where things can break.
3. A custom integration. Code written against each platform's API, hosted and monitored by you or your provider. It fits unusual rules (bundles, multi-warehouse allocation, B2B price lists) and costs more to build and maintain.
Whichever you choose, plan for missed messages. Shopify's own documentation says apps should not rely only on webhooks, because events can be missed through handler failures or downtime, and recommends periodic reconciliation jobs that fetch data to stay consistent (Shopify). That advice applies to every platform, and it matters more where connectivity or power can drop without warning.
The Nigerian details that trip people up
- VAT and withholding tax. Your store calculates VAT at checkout (the standard rate is 7.5 %), and some items may be zero-rated or exempt. Map each tax line to the right account in the ERP so your returns reconcile, and test an order for each tax treatment you sell, as your accountant classifies it. If customers deduct withholding tax when they pay your invoices, the ERP needs a place to record it, usually in the B2B flow rather than the retail one.
- Payouts arrive net of fees. Payment gateways deposit a lump sum after deducting fees, refunds and chargebacks. If you record each order as paid in full to the bank, your bank account will never reconcile. Use a clearing account for the processor and post fees separately. Our guide to bank feeds and ERP reconciliation covers this in detail.
- Other ways to pay. Many stores also take bank transfers (NIP) or pay on delivery. These arrive later than a card or wallet payment, and sometimes not at all, so decide when an order counts as paid and how unmatched transfers are cleared.
- Currencies. If you sell in US dollars as well as naira, decide where exchange differences are recorded and whether dollar payouts land in a dollar bank account.
- Addresses and delivery. Delivery addresses are often free text and phone numbers matter to couriers. Agree how states, delivery zones and courier rates are stored and synced, rather than treating logistics as an afterthought.
- Customer personal information. Customer names, addresses and order histories now live in two or more systems. Keep the flow limited to what each system needs, consistent with the data minimisation and security duties of the Nigeria Data Protection Act 2023 (NDPA), which the Nigeria Data Protection Commission enforces. This is general information, not legal advice.
What usually goes wrong
These are the patterns we see most often in store-to-ERP projects:
- SKU mismatches. A product exists as "TSHIRT-BLK-M" in the store and "TS-BK-MED" in the ERP. Orders fail or create stray items.
- Duplicate customers. Guest checkouts create a new customer record for every order. Agree a matching rule (usually email address or phone number) before go-live.
- Overselling. Stock syncs hourly, a popular item sells out in twenty minutes, and you owe customers apologies. Sync fast movers more often or hold a safety buffer.
- Refunds that never reach the books. Refunds issued in the store do not create credit notes in the ERP, so revenue and tax are overstated.
- Silent failures. An order fails to sync on Friday night and nobody notices until a customer calls. Every integration needs an error queue, an alert and a person who checks it.
Rather talk it through? If your team is re-keying orders or chasing stock mismatches, we can map your flows and recommend the lightest connection that will hold up. Talk to a Promatics specialist
When to bring in help
You can often set up a ready-made connector yourself if you have one store, one warehouse, a modest catalogue, simple tax (standard-rated VAT only) and someone comfortable checking error logs. Test thoroughly with real orders before switching it on.
A professional is worth it when you have several warehouses or sales channels, B2B and B2C pricing, bundles or kits, cross-border sales, a custom or heavily modified ERP, or high order volumes where an hour of broken sync costs real money. Help also pays off when nobody in-house can own the integration after launch. With our system integration service, we design the ownership map, build or configure the connection, test the awkward cases (partial refunds, split shipments, tax-exempt customers) and monitor it afterwards. If you are rebuilding the store itself, see eCommerce development.
Planning checklist
Ownership and identifiers
- Every record type has an agreed owner system and direction.
- Every item has one shared identifier used in both systems.
- A customer matching rule is agreed (for example, email address or phone number).
Money and tax
- Each tax line maps to the correct VAT account, and withholding tax has a place where it applies.
- Payouts post through a processor clearing account, with fees recorded separately.
- Bank transfers and pay-on-delivery orders have a clear rule for when they count as paid.
- Refunds and chargebacks create the right credit notes or entries.
Operations
- Stock sync frequency suits your fastest-selling items.
- Split shipments, backorders and returns have been tested.
- Delivery zones, states and courier rates have a home and a sync rule.
Reliability
- Failed records land in a visible queue with an alert.
- A scheduled reconciliation check compares store orders with ERP orders.
- A named person owns the integration and knows the manual fallback.
Sources and further reading
Product capabilities and guidance change. These are the primary sources this article relies on, checked on the review date above.
- Webhooks overview, Shopify Developer Documentation
- Shopify Integration, ERPNext documentation (Frappe)
- WooCommerce Integration, ERPNext documentation (Frappe)
- Nigeria Data Protection Commission (NDPA, GAID 2025 and guidance for data controllers and processors), Nigeria Data Protection Commission
This article is general information, not legal, accounting or security advice for your specific situation. Examples are hypothetical unless stated otherwise.