Higher Education Institutions are using various Management Information Systems as their main repository of the vast data that schools acquire from their stakeholders. On this dependency on technology the paradox of its misuse of platforms entailed breach on sensitive information, operational protocols, and even communication. Hence, creating a much demand for its heightened focus on safeguarding the institution's digital environments, through dynamic security measures and creating a much more technologically advanced landscape. As the call for safeguarding the digital environment, among Higher Education Institutions have resulted in strengthening their protection, however, even how much commercially offered software and systems are made available cyberthreats are still common to the said industry. Hence, the study purports to see the challenges in safeguarding the cybersecurity measurements being implemented by the HEIs in the National Capital Region that may stop or prevent cyberthreats and attacks as well as checking on the resiliency and awareness of its employees as they are the first line of defense. Using a descriptive-correlational approach, the data serves as the anchor-points of the proposed countermeasures that the cybersecurity framework has to offer.