Embedded systems that combine hardware and software components play a key role in ensuring the smooth operation of various devices and mechanisms. Virtual prototypes of embedded systems are actively used to improve the quality of development. Debugging and testing embedded systems software on virtual prototypes requires the creation of a debugging server. During testing, the debugging server processes a large number of requests from the operator or from the test script. Due to the growing number of devices being tested and the complexity of test scenarios, server response time is becoming critical. In this work, the optimization of the algorithm for decrypting debugging commands using linear and binary searches is considered. Main focus is on the implementation of a two-level command processing structure, which reduces the processing time of incoming requests. The productivity of software solutions was studied using experimental methods. To analyze the performance of the proposed method, experiments were conducted with measuring the execution time of command processing functions. It has been demonstrated that this approach allows significant improvement of the performance of command decryption function. In particular, the function execution time was reduced from 10.6 to 4.8 μs. The methods for algorithms performance measuring are described. The research results have shown that it is advisable to use the proposed solution to improve the performance of the debugging server.