Information security faces increasingly complex challenges, requiring innovative strategies to enhance system resilience against attacks. The concept of Moving Target Defense (MTD) emerges as a promising approach, as it complicates the identification and exploitation of vulnerabilities by dynamically modifying system configurations. Among the possible strategies, virtual machine migration and IP address relocation stand out, as well as the use of decoy servers that act as bait to mislead attackers and delay their progress. This study proposes a comparative evaluation of two distinct MTD methodologies, both modeled using Petri nets. The first approach relies on migration as a defensive strategy, considering three activation policies: time-based, event-based, and a hybrid approach that combines both. To strengthen the response to attacks, an intrusion detection system (IDS) was incorporated to identify malicious activities and trigger system migration as needed. The second approach analyzes the impact of using decoy servers combined with dynamic IP address migration to hinder the mapping of real servers and increase attacker uncertainty regarding the system’s topology. Simulation results indicate that the effectiveness of event-based detection policies heavily depends on the accuracy of the IDS, proving to be more advantageous when its precision exceeds 50%. Additionally, the hybrid approach demonstrated the highest efficiency in delaying attacker progress, balancing security and system performance. In the context of decoy servers, experiments revealed that introducing a higher number of decoys significantly increases the time required for a successful intrusion, extending it from 8 to up to 19 days. The interaction between attack probability and the number of decoys showed a direct impact on the rate of IP address changes, reinforcing the effectiveness of this strategy in enhancing system resilience. Thus, this study contributes to the understanding of the applicability of different MTD strategies, providing analysis into how migration policies and decoy server usage can be optimized to improve the security of computing infrastructures against cyber threats.