Embedded systems are widely used for implementing diverse Internet-of-Things (IoT) applications. These applications often deal with secret/sensitive data and encryption keys which can potentially be leaked through timing side-channel analysis. Runtime-based timing side-channel attacks are performed by measuring the time a code takes to execute and using that information to extract sensitive data. Effectively detecting such vulnerabilities with high precision and low false positives is a challenging task due to the runtime dependence of software code on the underlying hardware. Effectively fixing such vulnerabilities with low overhead is also non-trivial due to the diverse nature of embedded systems. In this article, we propose an automatic runtime side channel vulnerability detection and mitigation framework that not only considers the software code but also use the underlying hardware architecture information to tune the framework for more accurate vulnerability detection and system-specific tailored mitigation.