Ownership and control
WooCommerce is open source and sits on your hosting: the store, the data and the code are yours, and you can change anything. Shopify is renting a platform: you start faster and maintain nothing, but you work inside their rules and the data lives with them. If it matters that nobody can change the terms underneath you, Woo is the safer choice.
Costs over time
Shopify has a predictable monthly fee plus commissions, which is comfortable at the start. Woo has no platform fee, but you pay for hosting and maintenance, and sometimes individual extensions. The tipping point is turnover: at low volume Shopify looks cheaper, and as volume grows the percentages start to exceed the fixed cost of a Woo setup.
Payments and local reality
In many markets a significant share of customers still choose cash on delivery, and that has to work cleanly, with no workarounds. Woo gives full freedom here because payment and shipping rules are configured without platform limits. Card processing is chosen for the market and currency, covered in more detail in the piece on building an online store.
Migration
Leaving Woo is easy because the database and files are yours. Leaving Shopify is harder: products export, but the design, page URLs and part of the functionality are rebuilt. That is worth knowing at the start, not after two years.
Our recommendation
For most small and medium stores we recommend WooCommerce, for data ownership and predictable costs. Shopify is a legitimate choice when you want a fully hosted solution, have nobody for the technical side, and accept the monthly fee and commissions. There is no wrong choice, only a choice that does not match how you work.
We build online stores on both sides of this, tell us what you sell.