Background: Students' perceptions of learning environment is known as the most frequent construct related to their learning outcomes. Students' motivation in learning science (i.e. personal mastery goals orientation, self-efficacy, and task-value) and self-regulation are among the outcome variables that are affected by their perceptions of science learning environment (i.e. perceptions of their parents, school, and science teacher's mastery goals emphases, and peers' mastery goals orientation). Purpose: The purpose of the current study was to investigate the relations between environmental factors of students' perceptions of their parents, school, and science teacher's mastery goals emphases, peers' mastery goals orientation, and the internal constructs of students' motivational beliefs and self-regulation in science learning. Sample: Participants were 475 Iranian students at lower secondary schools. Design and method: A cross-sectional and correlational research design was employed in this study. Data were collected using a questionnaire consisted of three measures of perceptions of science learning environment, motivation, and self-regulation, which the participants were asked to complete. Structural equation modeling (SEM) and a bootstrap procedure were used to estimate the variables' direct and mediated relationships. Results: Results revealed that perceived peers' mastery goals orientation and perceived parents' mastery goals emphasis positively predicted personal mastery goals orientation. In addition, the results indicated that perceived teacher's mastery goals emphasis positively predicted task-value. Moreover, task-value and self-efficacy were found to have a significant direct effect on self-regulation. Conclusions: These findings provide novel insight into the role of environmental factors in students' motivation and self-regulation in science learning. In particular, science teachers are suggested to focus on encouraging students to adopt higher levels of mastery goals orientation in science learning activities, with regards to the significant mediating role of personal mastery goals orientation between perceptions of science learning environment and other motivational beliefs.