Microservice Architecture (MSA) is a popular approach to designing, implementing, and deploying complex software systems. However, MSA introduces inherent challenges associated with distributed systems—one of them is the detection and mitigation of security smells. This paper draws on recent works that identified and categorized security smells in MSAs to propose a novel end-to-end approach for resolving security smells in existing MSAs. To this end, the presented approach extends a modeling ecosystem for MSAs with (i) reconstruction capabilities that automatically map MSA source code to viewpoint-specific architecture models; (ii) validations that detect security smells from reconstructed models; and (iii) model refactorings that support the interactive resolution of security smells and solutions’ reflection back to source code. Our approach allows for (i) uncovering security smells, which originate from the combination of different places in source code with possibly heterogeneous purposes, technologies, and software languages; as well as (ii) clustering, reifying, and fixing smells using a level of abstraction that is directed towards MSA stakeholders. The applicability and effectiveness of our approach are evaluated utilizing a standard case study from MSA research.