The COVID-19 pandemic brought an education crisis that forced schools to abruptly shift to online distance learning. Regardless of the challenges in this migration, the teaching–learning process should continue. Self-regulated learning skills are essential in learning in an online environment; hence, the study aims to explore learners’ perception in an online learning environment, self-regulated learning skills, and academic achievement during a research methods course. Perception on the online learning environment, self-regulated learning skills, and academic achievement were collected periodically throughout the online course. The analysis included repeated measures of ANOVA to examine the trends between periods of measurement. A linear regression analysis was used to determine the impact of perception on the online learning environment to self-regulated learning. Results of repeated measures of ANOVA suggest a subtle decrease in the perception of the online learning environment at the start of the course. Still, ratings consistently increased viewing online distance learning the same with pre-quarantine set-up. On the other hand, self-regulated learning remained virtually the same throughout the implementation of research methods online course. A rise in the learning playlist scores has been observed at the start of the research methods course, but scores began to decline at the latter phases of the course. Results of regression analysis imply the influence of perception on the online learning environment on self-regulated learning skills. However, perception does not affect learners’ academic achievement. The study recommends using strategies to further develop perseverance in adjusting to online learning amid initial setbacks. Also, interventions specific to improving learners’ self-regulated learning skills are highly recommended.