Secure multiparty computation (MPC) does help here.

Suppose you have multiple organizations that want to run some computation on their joint data, without revealing their data to each other. Each organization has their own machine that runs the MPC protocol. They have full control over their machine, and can inspect that the code correctly executes the protocol. Only once all organizations agree, will the computation take place, and within the security model of the protocol, it is guaranteed that only the correct computation output is revealed to the designated parties.