The expansion of social media has influenced the ways in which adolescents develop their identities, particularly their religious identity. Virtual environments provide access to diverse religious resources while also exposing adolescents to different value systems and media content. In this context, media literacy may play an important role in adolescents’ religious identity. This study aimed to develop a structural model of adolescents’ religious identity, focusing on the direct role of media literacy, the mediating role of virtual messenger use, and the moderating role of dominant messenger type. The study was applied in purpose and descriptive-correlational in design, using structural equation modeling. The statistical population consisted of adolescents aged 15–18 years in the Qasemabad district of Mashhad, Iran. A total of 300 participants were selected through convenience sampling. Data were collected using the Media Literacy Questionnaire (Falsafi, 2014), Religious Identity Questionnaire (Khoshabi, 2011), and a researcher-developed measure of messenger use and dominant messenger type. Data were analyzed using AMOS 24. The proposed model showed acceptable fit (CFI = .93, RMSEA = .068). Media literacy had a significant positive direct effect on religious identity (β = .35, p < .05) and was positively associated with messenger use (β = .38, p < .05). Messenger use was negatively associated with religious identity (β = −.22, p < .05) and partially mediated the relationship between media literacy and religious identity (indirect effect β = −.06, 95% CI [−.12, −.02]). Multi-group analysis indicated significant differences between users predominantly using domestic and foreign messengers in both structural paths. Overall, the model explained 52% of the variance in religious identity. The findings highlight the importance of considering cognitive, behavioral, and media-environmental factors in understanding adolescents’ religious identity in digital contexts.