Where do I apply and who decides on a Swiss self-employment permit for non-EU nationals?

The process is canton-led at the front end: you lodge your application with the competent cantonal labour-market and migration authorities, who assess the business case against the economic-interest and priority tests.

For third-country nationals, federal approval is also part of the admission, reflecting the national quotas and conditions under the FNIA. Detailed criteria are set out in the FNIA directives, and because requirements differ by canton, it is best to confirm the exact procedure with the authority responsible for where you plan to base your business.