Science self-efficacy, a student's confidence in being able to perform scientific practices, interacts with science identity and outcomes expectations, leading to improved performance in science courses, persistence in science majors, and ultimately, the pursuit of advanced training in the sciences. Inquiry-based laboratory courses have been shown to improve undergraduate student self-efficacy, but the mechanisms involved and specific components of instructional practices that lead to improved self-efficacy are not clear. In the current study, we determined whether student and faculty perceptions of laboratory instructional practices (scientific synthesis, science process skills, and instructor-directed teaching) were related to postsemester self-efficacy across 19 guided-inquiry laboratory courses from 11 different institutions. Self-efficacy related to science literacy increased significantly from the beginning of the semester to the end of the semester. Variation in individual student perceptions of instructional practices within a course were significantly related to differences in student self-efficacy at the end of the semester, but not average student perceptions or faculty perceptions of their own practices across courses. The importance of individual student perceptions suggests that faculty should engage with students during curricular development. Furthermore, faculty need to use noncontent talk to reinforce the science practices students are engaging in during inquiry-based laboratory courses.