Computer programming e-learners faced stressful life circumstances and educational changes that affected the world during the COVID-19 pandemic. As the cognitive model of flourishing focuses on cognitions rather than situations themselves, it was deemed significant to identify peer-to-peer confirmation, positive automatic thoughts, flourishing, and the links between these study variables in a group of computer programming e-learners and compare the results with other e-learners. This study applied the Flourishing Scale (FS), the Automatic Thoughts Questionnaire—Positive (ATQP), and the Student-to-Student Confirmation Scale. The sample consisted of 453 e-learners, including 211 computer programming e-learners. The results revealed that computer programming e-learners differed from other e-learners in flourishing, positive daily functioning, and peer-to-peer confirmation. In both samples, positive daily functioning and positive future expectations predicted self-reported flourishing. Positive automatic thoughts and flourishing predicted peer-to-peer confirmation just in the group of computer programming e-learners. The SEM analysis revealed that peer-to-peer confirmation and positive automatic thoughts explained 57.4% of the variance of flourishing in the computer programming e-learners group and 9.3% of the variance in the social sciences e-learners group, χ² = 81.320, df = 36, p < 0.001; NFI = 0.963; TLI = 0.967; CFI = 0.979; RMSEA = 0.075 [0.053–0.096]; SRMR = 0.033. The findings signify the importance of peer-to-peer confirmation and positive thoughts for computer programming e-learners’ psychological well-being. Nevertheless, the results of this particular study should be regarded with caution due to the relatively small sample size and other limitations. In the future, it would be valuable to identify the underlying mechanisms and the added value of positive states such as flow, which have recently received the increased attention of researchers.