The classroom environment influences students academic outcomes, but it is often students perceptions that shape their classroom experiences. Our study examined the extent to which observed classroom environment features shaped perceptions of the classroom, and explained levels of, and changes in, girls motivation in junior secondary school science classes across two school terms. Girls have been found to feel less capable than boys and to under-participate in science classrooms, even though their achievement levels are similar. Four teachers and five of their classrooms of students (N = 52) reported their perceptions of the classroom environment, and trained observers rated the actual classroom environment. Students also completed questions regarding their motivations for science at both time points. Hierarchical linear modelling showed that students perceptions of classroom structure were very important and exerted significant influence on science motivations. All of the six observed classroom dimensions affected students extrinsic utility value, via perceptions of structure. Other classroom dimensions showed particular patterns of relationship with motivations. Teachers perceptions of the classroom environment were often more positive than those of the students, which is congruent with previous research. The findings have implications for retaining girls in science and, thereby, addressing the gender gap in science-related vocations.