Anomaly detection can ensure the operational integrity of control systems by identifying issues such as faulty sensors and false data injection attacks. At the same time, we need privacy to protect personal data and limit the information attackers can get about the operation of a system. However, anomaly detection and privacy can sometimes be at odds, as monitoring the system’s behavior is impeded by data hiding. Cryptographic tools such as garbled circuits and homomorphic encryption can help, but each of these is best suited for certain different types of computation. Control with anomaly detection requires both types of computations so a naive cryptographic implementation might be inefficient. To address these challenges, we propose and implement protocols for privacy-preserving anomaly detection in a linear control system using garbled circuits, homomorphic encryption, and a combination of the two. In doing so, we show how to distribute private computations between the system and the controller to reduce the amount of computation–in particular at the low-power system. Finally, we systematically compare our proposed protocols in terms of precision, computation, and communication costs.