While gamification has been extensively examined as an innovative teaching strategy, its potential to strengthen reading comprehension, critical thinking, and self-directed learning (SDL) in Islamic higher education has not been fully explored. Much of the existing research focuses primarily on its motivational impact, with less attention given to how gamified learning management system (LMS) environments can simultaneously support cognitive and metacognitive development. To address this gap, the present study evaluated the effectiveness of an LMS-based gamified reading comprehension course on undergraduate students’ learning outcomes at STAI Diponegoro Tulungagung, Indonesia. A quasi-experimental design was applied, involving 70 students who were randomly assigned to an experimental group (n = 35) and a control group (n = 35). Data were collected through pretest and posttest on reading comprehension and critical thinking, a structured SDL questionnaire based on Garrison’s (1997) framework (self-management, self-motivation, and self-monitoring), and follow-up interviews with six purposively selected students from the experimental group. Results indicated that students exposed to the gamified LMS course showed significantly higher gains in comprehension, critical thinking, and SDL than those in the control group. Qualitative findings further suggested that gamification fostered continuous engagement and sustained motivation, though certain challenges, including technological constraints and external distractions. Overall, the study underscores the promise of integrating gamification into LMS-based reading courses to support cognitive, affective, and metacognitive advancement in Islamic higher education.