Michal Kosicki Thanks for posting your question in Microsoft Q&A. Currently, FHIR service in Azure Health Data Services does not support B2C as described in the doc: Can I use Azure AD B2C with the FHIR service?
I couldn't find info about Azure Health Data Services Toolkit supporting B2C which is same as SMART on FHIR Proxy. You can explore option of using Azure API Management in front of FHIR servers to expose SMART endpoints and article: Publish SMART on FHIR OAuth2 URLs using Azure API Management would help with that.
I hope this helps and let us know if you have any other questions.