In a learning environment, a low student-lecturer ratio is considered a practical solution by many educational institutions. However, the number of students in information technology is increasing every year. This could lead to a significant increase in the workload of lecturers, who need to evaluate assignments, quizzes and projects. Hence, it is desirable that an automated assessment tool is used to lessen their workload. In the era where mobile devices are getting popularity, the high demand to execute suitable quality code is there and the cost is on the processing power of the CPU which has a direct implication on the power source or the battery used. With various implementations of cryptography algorithms available, many of them could satisfy different level of needs. In this research, we introduce the architecture for a multi-layered security of automated assessment of programming code. First, we review the existing research studies in the area. We describe the features of the tool, as part of a complex elearning environment. We also discuss the implementation of security, to protect data transmission and storage used by the tool. Challenges the system might face and the potential solutions, are also described.