The COVID-19 pandemic has led to the widespread adoption of flexible learning, which allows students to access educational materials and participate in classes remotely. Self-determination theory, a focus of this article, promotes self-motivation in the digital world of flexible learning. This study aimed to determine the link between undergraduate students' satisfaction with flexible learning and the following variables: (a) student-instructor connection; (b) the technological competency of students and instructors; and (c) the association between students' satisfaction and health and humanities courses. A descriptive correlational research design and binary logistic regression model were used to analyse data from 610 undergraduate students (53% female, 47% male) enrolled in at least one flexible learning course at a university in Jordan in 2020/2021, during the COVID-19 pandemic. The study found that 63.4% of participants were enrolled in three or more flexible learning courses, while 27.2% were enrolled in two or more. However, 52.8% expressed dissatisfaction with these courses. Additionally, the study showed a moderately positive relationship between students' satisfaction and connection to their instructor, as well as a significant positive relationship between student-instructor connection and students' technological competency. Students in humanities courses were more satisfied and did better academically with flexible learning than those in health courses. High technological competency in instructors led to two times greater satisfaction with flexible learning and a positive perception of online education quality. Finally, a significant difference was found between students' attitudes towards flexible learning and their courses in humanities and health. Thus, applying self-determination theory is crucial for designing effective online learning during challenging times.