The COVID-19 pandemic and the rapid development of technologies have forced restructuring education at all levels. This change from traditional to digital learning demanded that teachers and students possess higher digital literacy. Moreover, it required them to be aware of the importance of security and its countermeasures to protect e-learning systems. The aim of this paper was twofold. First, it focused on security issues when using Moodle, Zoom. Blackboard, and edX. Furthermore, it offers best practices to address security threats and cyber-attacks from the outside network to e-learning systems. From this study, a cryptography mechanism arises as the best technique to protect the confidentiality, integrity, and authentication (CIA) of data on the e-platforms. However, it is not strong enough to mitigate cybersecurity attacks in e-learning systems. For that reason, it is suggested that the cryptography mechanism needs to be combined with other techniques such as biometric authentication, firewalls, IDS, digital watermarking, and security process models.