The objective of this study is to create an advanced cloud computing security system that addresses the security vulnerabilities inherent in existing authentication processes in communication systems. Specifically, the study developed an application-based multi-layer and multi-factor authentication (MFA) program that enhances cloud security measures. The system presented an improved approach to cloud computing security through the implementation of application-based multi-factor authentication (MFA). By leveraging encryption techniques, the system guarantees secure access based on user profiles. These profiles consist of valid usernames, passwords, and token numbers generated by the application. In addition, the system enhances security by integrating the Time-based One-Time Password (TOTP) algorithm (IETF RFC 6238) with location checks, augmenting the overall protection measures. A thorough testing procedure was carried out on the system, with a specific focus on a test web application hosted on the cloud server. The result validated the efficacy of all three authentication factors integrated within the application.