This question usually arrives framed as an SEO one, and SEO is close to the least important input. Both platforms can rank perfectly well when configured properly. The decision is operational.
Choose Shopify if
You want the store running quickly with minimal technical overhead. Hosting, security, updates and payments are handled, the admin is genuinely good, and a small team can run it without a developer on call. For catalogues in the hundreds and standard product types, this is often the right answer and the honest recommendation even though it involves less work for me.
Choose WooCommerce if
You need control: complex product configurations, custom checkout logic, bespoke integrations, or content and commerce tightly interwoven, which is where WordPress genuinely excels. It also has no platform transaction fees and lower running costs at volume, at the price of you owning hosting, security and updates.
The SEO differences, honestly
Shopify’s URL structure is rigid: collections and products sit in fixed paths whether or not that suits your architecture. It is a real limitation and rarely a decisive one. WooCommerce gives full URL control and, in exchange, more ways to create crawl bloat through unmanaged filters and attributes. Neither platform ranks better than the other; configuration decides it.
The cost picture over three years
Shopify’s subscription and transaction fees are predictable and rise with revenue. WooCommerce’s hosting and maintenance are lower but include the cost of someone being responsible. Model three years rather than three months, and include the value of your own time, which is where most comparisons quietly cheat.
What actually decides it
Who maintains the store day to day. If that is a non-technical team, Shopify. If you have development capacity or need flexibility no theme will give you, WooCommerce. Choosing on SEO grounds is optimising the wrong variable, and either way the e-commerce SEO work that follows is broadly the same.