The unprecedented situation of the COVID-19 pandemic has caused the closure of universities worldwide and has forced the transition to online learning. This exceptional context compels us to understand students' experience with online learning. Previous literature identifies relevant factors that intervene in the online education experience and can affect students' academic development. One of the main concerns is the students' mental health, given the lockdown restrictions under which classes have been conducted. Furthermore, the impact of the prolonged lockdown and the pandemic fatigue on university students and their academic experience is still unclear. This study delves into engineering undergraduate students' online education experience during the COVID-19 pandemic and its emotional impact across time. With this aim, a questionnaire was distributed to second, third, and fourth-year engineering undergraduate students at two time points, approximately six months apart. The results show significant differences in students' connection with other students and teachers, workspace conditions, and boredom between time points. Besides, the findings indicate significant correlations between academic development and quality of online classes, adaptation of the course, workspace conditions, and connection with other students and teachers, and also between students' emotions and connection with other students and teachers. Finally, the study identifies best practices carried out during online teaching that will be of value for future courses and engineering education beyond the pandemic situation, amongst which those related to effective communication with teachers stand out.