Students' motivational beliefs about physics can influence their learning outcomes as well as retention in their majors and career choices. Moreover, due to societal stereotypes and biases about who belongs in physics and can succeed in physics, women often have lower motivational beliefs about physics than men. The expectancy-value theory emphasizes the importance of self-efficacy and value in predicting students' short- and long-term academic and professional outcomes. Investigating how the perception of learning environment in introductory physics courses for the engineering, physical science, and mathematics majors in their first year of college predicts the motivational beliefs of women and men can be useful in making the learning environments equitable and inclusive so that the underrepresented students, e.g., women, are not disadvantaged. In this study, we adapt prior identity framework to investigate how the learning environment predicts students' physics self-efficacy, interest, and identity by controlling for their self-efficacy and interest at the beginning of a calculus-based introductory physics course. We surveyed 1203 students, 35% of whom identified as women. We found signatures of inequitable and noninclusive learning environment in that not only were female students' physics self-efficacy and interest lower than male students' at the beginning of the course, but the gender gaps in these motivational constructs became even larger by the end of the course. Analysis revealed that the decrease in students' physics self-efficacy and interest were mediated by the learning environment and predicted students' physics identity. Moreover, perceived recognition played a major role in predicting students' physics identity.