Performance evaluation of multi-agent systems (MAS) embraces several challenges due to uncertain operational environments, such as software/hardware failures and unfaithful communications that facilitate the spread of deceptive messages. One way to smooth the impact of reliability and security potential issues in MAS is to enforce different coordination mechanisms among agents (i.e., coordinating multiple agents that need to perform a sequence of actions to maximize a system-level reward), and evaluate their efficiency. In this paper, we propose a tool-based approach, namely COORDINATE, that simulates and compares the performance characteristics of different coordination mechanisms for MAS while considering fault-tolerant and corrupted agents. A Smart Hospital is adopted as illustrative example to show the need of performance-based analysis results pointing out which coordination mechanism is more efficient. Experimental results indicate that the inter-arrival time of tasks to be accomplished, the failure probability of agents, and the ratio of faithful to malicious agents contribute to determining the efficiency of different coordination mechanisms. When varying these parameters in the considered scenarios, the system latency can be reduced up to 4.2× by selecting the optimal coordination mechanism. This way, software developers are informed on the system peculiarities that trigger the switching among such coordination mechanisms for a performance-based optimal solution.