Cloud multi-factor authentication is a critical security measure that helps strengthen cloud security from unauthorized access and data breaches. Multi-factor authentication verifies that authentic cloud users are only authorized to access cloud apps, data, services, and resources, making it more secure for enterprises and less inconvenient for users. The number of authentication factors varies based on the security framework’s architecture and the required security level. Therefore, implementing a secured multi-factor authentication framework in a cloud platform is a challenging process. In this paper, we developed an adaptive multi-factor multi-layer authentication framework that embeds an access control and intrusion detection mechanisms with an automated selection of authentication methods. The core objective is to enhance a secured cloud platform with low false positive alarms that makes it more difficult for intruders to access the cloud system. To enhance the authentication mechanism and reduce false alarms, multiple authentication factors that include the length, validity, and value of the user factor is implemented with a user’s geolocation and user’s browser confirmation method that increase the identity verification of cloud users. An additional AES-based encryption component is applied to data, which are protected from being disclosed. The AES encryption mechanism is implemented to conceal the login information on the directory provider of the cloud. The proposed framework demonstrated excellent performance in identifying potentially malicious users and intruders, thereby effectively preventing any intentional attacks on the cloud services and data.