This is currently not easily achievable. However, it is possible if you are ok with creating multiple Google accounts, one per Matomo instance.

Begin by creating data sources for each Matomo instance within each of your Google accounts. Then visit the Data sources tab in each Looker Studio dashboard and click the more icon represented by three dots at the end of the row for your Matomo data source.

Screenshot showing the Data source section in Looker Studio.

Then click Share within the sub-menu and invite your primary Google account to use the data source.

Screenshot showing the Looker Studio share menu for Data sources.

Repeat this process for each additional Matomo instance within each additional Google account.

Once your primary account has been invited to share all of the Data sources from the additional accounts, you can then use the primary account to create reports using the additional shared data sources for multiple Matomo instances.

Previous FAQ: How do I embed Matomo reports from multiple sites in Looker Studio?