As interest in Internet of Things environments rapidly increases throughout the IT convergence field, compatibility with mobile devices must be provided to enable personalized services. The security of mobile platforms and applications is critical because security vulnerabilities of mobile devices can be spread to all things in these environments. Android, the leading open mobile platform, has long used the Dalvik virtual machine as its runtime system. However, it has recently been completely replaced by a new runtime system, namely Android Runtime (ART). The change from Android’s Dalvik to ART means that the existing Dalvik bytecode-based application execution structure has been changed to a machine code-based application execution structure. Consequently, a detailed understanding of ART, such as new file formats and execution switching methods between codes, is required from the viewpoint of application security. In this paper, we demonstrate that an existing Dalvik-based application vulnerability can be exploited as-is in ART. This is because existing Dalvik executable files coexist in the ART executable file, and these Dalvik bytecodes and compiled machine codes have one-to-one mapping relationships. We then propose an ART-based application protection scheme to secure this by dynamically eliminating the one-to-one mapping. In addition, the proposed scheme is implemented to evaluate its reverse engineering resistance and performance through experiments.