The short answer
Mikro Shopify integration is the automatic transfer of stock cards, warehouse stock and prices from Mikro to your Shopify store, and of Shopify orders, customers and payments into Mikro as orders, customer accounts and invoices. The connection is built through a middleware layer between Mikro's API service and the Shopify GraphQL Admin API and webhooks.
Mikro integrations are most common among businesses running Mikro Jump and Mikro Fly. A standard B2C store typically goes live in 6–10 weeks; projects with B2B or multiple warehouses take 10–14 weeks.
This guide draws on the field experience of Byte Digital, a Shopify Plus Partner that has served Shopify brands for 7 years.
Which data is synchronised between Mikro and Shopify?
Stock cards, stock and prices flow from Mikro to Shopify; orders, customer accounts and payments flow from Shopify to Mikro.
Data | Direction | Frequency | Mikro side | Shopify side |
|---|---|---|---|---|
Stock card | Mikro → Shopify | On change | Stock code, name, unit, main group / department | Product, collection, metafields |
Variant | Mikro → Shopify | On change | Size-colour tracked stock or separate stock cards | ProductVariant |
Barcode | Mikro → Shopify | On change | Barcode definitions | Variant barcode and SKU |
Stock level | Mikro → Shopify | Every 5–15 minutes | Stock per warehouse | InventoryLevel, Location |
Price | Mikro → Shopify | On change | Sales price lists | Price, compare-at price |
Order | Shopify → Mikro | Real time (webhook) | Customer order | Order |
Customer | Shopify → Mikro | With the order | Customer account card | Customer |
Payment | Shopify → Mikro | With the order | Credit card collection, bank account | Transaction |
Shipment and invoice | Mikro → Shopify | On dispatch | Dispatch note, invoice, e-invoice / e-archive | Fulfillment, tracking number |
Return | Two-way | Event-driven | Return invoice / dispatch note | Return, Refund |
Which Mikro product do you use? Mikro integration interfaces
The Mikro product family is split by business size into Run, Jump and Fly (kobitime), and the depth of the Shopify integration varies accordingly.
Mikro product | Typical users | What it means for a Shopify integration |
|---|---|---|
Mikro Run | Sole traders and small businesses; bookkeeping, invoicing, stock | Simple stock and order transfer; an off-the-shelf integrator is usually enough |
Mikro Jump | Mid-sized businesses opening branches | The most common scenario; full integration with multiple warehouses, price lists and customer accounts |
Mikro Fly | Large businesses and industrial companies | B2B, manufacturing and multi-company structures; custom middleware is usually needed |
There are two ways to connect to Mikro:
Mikro API service: Writes records such as orders, customer accounts and payments through Mikro's business rules. This is the recommended method for writes; confirm the service's installation and licensing with your Mikro partner.
SQL Server database: Reading stock, prices and stock cards from Mikro's database is fast and practical. Writing directly to tables, however, can break the integration on Mikro updates and put accounting consistency at risk; use it for reads only.
Mikro Shopify integration methods
An off-the-shelf integrator suits Mikro Run and simple Jump setups; a multichannel platform suits businesses also connecting marketplaces; custom middleware is the right choice for Fly and B2B scenarios.
Method | When to choose it | Setup time | Flexibility | Ongoing cost |
|---|---|---|---|---|
Off-the-shelf Mikro integrator | Single warehouse, standard order and invoice flow | 2–5 weeks | Low–medium | Monthly licence |
Multichannel integration platform | When marketplaces are also connected to Mikro | 4–8 weeks | Medium | Monthly licence, possibly per-order fees |
Custom-built middleware | Mikro Fly, B2B prices and payment terms, multiple warehouses, high volume | 6–14 weeks | Highest | Hosting + maintenance |
Mikro usually runs on a server inside the company, so the architecture has two parts: a connector service running close to the Mikro server that reads and writes data, and a cloud middleware that receives Shopify webhooks and holds the order queue. The two parts talk over an encrypted connection, and the Mikro server is never exposed directly to the internet.
What to watch for in a Mikro integration
The most time-consuming work in a Mikro integration is getting stock cards ready for e-commerce and settling the accounting decisions.
Stock card clean-up: Stock names in Mikro are usually abbreviated and warehouse-oriented. Customer-facing product names, descriptions and images should be managed separately in Shopify; Mikro should only be the source of codes, barcodes, stock and prices.
Which items are sold online? Use an "online" flag or a separate group on the stock card so that only sellable products are sent to Shopify.
Customer account strategy: One e-commerce account for individual buyers and separate accounts by tax number for corporate buyers makes both the e-invoice / e-archive split and reporting easier.
e-Invoice and e-Archive: Invoices are issued from Mikro through the e-transformation service Mikro works with. The Shopify checkout should collect corporate invoice fields (company name, tax office, tax number) and pass them with the order.
VAT and rounding: VAT-inclusive Shopify prices and discounts must be distributed so that each line produces the same amount in Mikro.
Payments and instalments: Payments from a virtual POS or payment provider must be posted to the correct bank account with commission and instalment details.
Mikro Shopify integration step by step: timeline and cost
A standard B2C store goes live in 6–10 weeks; projects with B2B or multiple warehouses take 10–14 weeks.
Discovery (1 week): Mikro product and version, warehouses, price lists, customer account and invoicing strategy are defined.
Stock card preparation and mapping (1–3 weeks): Items to sell online are selected; stock codes are mapped to SKUs, warehouses to locations and payment methods to bank accounts.
Development (2–5 weeks): Stock and prices first, then orders, customer accounts and payments, finally returns and invoicing.
Testing (1–2 weeks): End-to-end scenarios and accounting checks in a Mikro test company.
Go-live and hypercare (2–4 weeks): A daily error report is tracked until the first month-end close.
The main cost drivers are the Mikro product (Run, Jump or Fly), whether the API service is already in place, how much clean-up the stock cards need, the number of warehouses, B2B account and pricing structure, and whether marketplaces are included in the same project.
The 6 most common mistakes in Mikro Shopify integration
Most problems in Mikro projects come from building the integration to write directly to the database and from transferring stock cards as they are.
Writing to Mikro tables with SQL: Creating orders and customer accounts outside the API corrupts balances and stock calculations, and the integration stops working after a Mikro update.
Showing stock card names to customers: Abbreviated names like "KZK TSHRT BYZ M" left as Shopify product titles hurt both conversion and SEO.
Opening an account for every individual buyer: Thousands of unnecessary account cards and duplicate records are created.
Exposing the Mikro server to the internet: This creates a security hole; the connection should run through a service inside the company network.
Updating stock only overnight: Store and wholesale sales during the day are not reflected in Shopify.
Not planning the fiscal period change: Which company and period the integration writes to at year-end must be set in advance.
Mikro Shopify integration with Byte Digital
Byte Digital is an Istanbul-based Shopify Plus Partner that has provided Shopify migration, theme development and ERP integration services to leading Turkish brands for 7 years. Working alongside your finance team, we connect Mikro's stock, account and warehouse structure correctly to Shopify's product, order and payment flow.
Share the Mikro product you use (Run, Jump or Fly), your monthly order volume and the flows you want to connect, and we will prepare a free pre-assessment with the right method, timeline and an estimated budget.
Request a free Mikro Shopify pre-assessment →
Frequently asked questions
Can Mikro be integrated with Shopify?
Yes. Mikro Run, Jump and Fly can be integrated with Shopify through Mikro's API service and database. Stock, prices and stock cards flow automatically from Mikro to Shopify; orders, customer accounts and payments flow from Shopify to Mikro.
How long does a Mikro Shopify integration take?
For a standard B2C store, 6–10 weeks. Simple setups with an off-the-shelf integrator take 2–5 weeks; projects with B2B and multiple warehouses take 10–14 weeks.
Which Mikro product do I need for the integration?
Run, Jump and Fly can all be integrated. Jump or Fly is the better fit for businesses that need multiple warehouses, price lists and B2B.
How do Shopify orders reach Mikro?
A Shopify order reaches the middleware instantly via webhook and is written to Mikro as a customer order. On shipment it becomes a dispatch note and invoice; the tracking number is sent back to Shopify and the customer is notified.
Is the e-invoice issued from Mikro or from Shopify?
e-Invoices and e-archive invoices are issued from Mikro through the company's e-transformation service. Shopify's job is to pass the corporate invoice details in full with the order.
Our Mikro server is on-premise. How does it talk to cloud-based Shopify?
A connector service running close to the Mikro server inside the company opens an encrypted connection to the cloud middleware. The integration works without exposing the Mikro server to the internet.
Sources
kobitime — Mikro Yazılım product family (Run, Jump, Fly)
