Student grades and motivational outcomes in introductory physics courses can influence their retention in science, technology, engineering, and mathematics disciplines and future career aspirations. We surveyed students in mandatory large introductory level algebra-based physics courses for bioscience majors at a large research university. The study investigates how students' perception of their learning environment, including their sense of belonging, peer interactions, and perceived recognition by instructors, predicts male and female students' grade, self-efficacy, interest, and identity at the end of physics 2, controlling for their high school GPA and SAT math scores. We find that although women outnumbered men in these courses, women had worse outcomes than men. Moreover, using structural equation modeling, we find that all factors in students' perception of their learning environment are essential to predicting their self-efficacy, interest, grade, and identity at the end of physics 2. The findings pertaining to gender differences call into question equity in learning in these physics courses and how the perception of the learning environment predicts the outcomes and can be useful for creating an equitable and inclusive learning environment to help all students excel in these algebra-based physics courses.