E-learning is an emerging trend in most universities. Due to COVID-19, many universities adopted e-learning. With the sudden adoption and implementation of e-learning, learners had to undergo learning on how to learn and take examinations electronically, which could have increased cognitive load in their learning experience. Without regular, face to face interactions with their peers, lecturers and tutors, learners could have also experienced challenges in keeping themselves motivated to study, carry out their course projects and prepare for examinations. Though cognitive load and motivation are essential elements in ensuring effective e-learning, there are not many studies that have looked at the impact of e-learning implementations on these elements for learners. This study therefore aimed to measure the cognitive load and motivation of e-learners and see the relationship between support provided to learners and cognitive load and motivation. The study was carried out in two Kenyan universities. A total of 314 learners participated in the study. The study revealed that e-learners experienced average cognitive load and above average motivation levels. Learners who received support reported lower intrinsic and extraneous cognitive load and higher germane and motivation levels. The study concludes that, learners in e-learning environment are experiencing average cognitive loads and above average motivation and therefore require instructional designers to implement strategies to reduce the cognitive load and improve motivation.