Background Mobile‐assisted language learning (MALL) has long been advocated to promote students' language study outcomes. However, little is known about how using instant messaging applications (an example of MALL) affect student motivation, language anxiety, and actual achievement. Objectives To help close this gap, we have conducted a quasi‐experimental study, in which we have used self‐determination theory to test a mediational process model, in an effort to understand the psychological mechanisms that underlie the effect of instant messaging applications on student outcomes. Methods Two groups of Saudi undergraduate students (N = 447) were recruited to participate in the study. Participants under the experimental condition were invited to engage in language‐related tasks with their teacher outside of class through the WhatsApp application, whereas participants under the control condition received standard teaching. We applied partial least square structural equation modelling (PLS‐SEM) to test our model. Results and Conclusions The results of the PLS‐SEM showed that the total effects of using instant messaging applications on autonomous motivation and L2 achievement were significant but that language anxiety was influenced only indirectly and negatively through language achievement. Also, the PLS‐SEM showed that our results have strong predcitive power indicating support for external validity. Implications Our results show that instant messaging applications can be used to facilitate interest and achievement and to decrease anxiety. Furthermore, we are contributing to L2 methodological literature by using applications of PLS‐SEM in experimental designs that can help researchers and practitioners of motivational processes. Lay Description What is already known about this topic Using WhatsApp and more broadly instant messaging applications are conceived to be motivating in language teaching context Studies indicate students are inclined toward using these applications in language learning Research shows that using WhatsApp is easy to apply for language teaching purposes What this paper adds The study examined the effect of using WhatsApp on language learners' motivation, achievement, and language anxiety A pre‐ and post‐test approach with experimental and control condition has been used to evaluate the effect more accurately The study employs Self‐determination Theory as a theoretical framework for testing a motivational process model Results show that using WhatsApp predicted the outcomes directly and indirectly Implications for practice and/or policy WhatsApp can significantly encourage university students to better learning of the language skills especially in times where face‐to‐face communication is limited WhatsApp is conditioned by the guidance of instructors, their ongoing formative and summative assessment WhatsApp appears to allow students enjoy their learning process due to the opportunities for collaborative work and constant exchange of content