WhatsApp (WA) has become increasingly popular in second language (L2) instructional practices, primarily for assessing L2 learners’ outcomes. Despite this popularity, there remains a significant gap in the literature regarding well-documented inquiries into the cognitive processes and reading comprehension of L2 learners. This study aimed to explain L2 learners’ reading comprehension abilities, and explore their cognitive processes between L2 learners who were taught using WA reading groups and those taught using the traditional group-driven reading approach. A mixed quantitative using an experimental design with 32 learners (12 males and 20 females) and a qualitative design was applied to address the two research purposes. The study results illustrated that learners' cognitive process in the WA reading group was effective, and their reading comprehension scores were higher than the traditional reading group. The effective cognitive strategies were visualized from learners’ WA chat histories. The WA reading group's cognitive process involved content discussion, self-reflection, and interpretation during online reading activities. They did not discuss from word to passage, but they tended to discuss the text's content and logical flow without finding the same difficult word for all group members. Conversely, the traditional reading group cognitive processes were less effective since the group member roles were not identified, such as all learners starting to find similar unfamiliar words and then discussing them again before interpreting the content of the texts. Study limitations and pedagogical implications from the study are adequately discussed.