The concept of e-learning and its implementation have grown significantly in the past decade. The educationalist considered this adoption a valuable solution in the field of education to organize a more effective learning system supporting the traditional one. With the options of e-learning platforms and tools, many institutes from various sectors, especially schools and higher education institutes, have used Moodle as their choice of platform for the institute's e-learning needs. Regarding the information, this article aims to (1) identify the challenges faced in Moodle implementation for online learning; (2) identify some apparent trends in Moodle adoption and innovation in e-learning for future research potential. This paper then proposed theoretical contributions regarding Moodle and e-learning. The approach used in this study adopted from Kitchenham to review research sources in a systematized order followed by extended analytical review to verify each source in terms of compatibility with research questions. We identified the challenges in Moodle implementation and the corresponding research trends of e-Learning System with Moodle in 3 key themes: General topic of Moodle, Moodle adoption, and innovations in the usage of Moodle and its development.