With the rapid growth of Internet of Things (IoT) systems, ensuring robust security measures has become paramount. Microservices Architecture (MSA) has emerged as a promising approach for enhancing IoT systems security, yet its adoption in this context lacks comprehensive analysis. This systematic review addresses this research gap by examining the incorporation of MSA in IoT systems from 2010 to 2024. From an initial pool of 4388 studies, selected articles underwent thorough quality assessment with weighted critical appraisal questions and a defined inclusion threshold. This study represents the first comprehensive systematic review to investigate the potential of microservices in IoT, with a particular focus on security aspects. The review explores the merits of MSA, highlighting twelve benefits, eight key challenges, and eight security risks. Additionally, the eight best practices for implementing MSA in IoT systems are extracted. The findings underscore MSA’s utility in fortifying IoT security while also acknowledging complexities and potential vulnerabilities. Moreover, the study calls attention to the importance of incorporating complementary technologies including blockchain and machine learning to address identified gaps effectively. Finally, we propose a taxonomic classification for Microservice-based IoT security patterns, facilitating the categorization and organization of security measures in this context. Such a review can help researchers and practitioners identify existing gaps, highlight potential research directions, and provide guidelines for designing secure and efficient microservice-based IoT systems.