There have been multiple national calls for curricular reform in science, technology, engineering, and mathematics (STEM), including a need to instill democratic skills in students. Democratic skill building can be embedded in STEM classrooms through intentional “deliberative pedagogies” that include communication, collaboration, and application of information. We developed and implemented a deliberative pedagogy, Deliberative Democracy (DD), for introductory majors and nonmajors undergraduate biology courses and took a longitudinal, qualitative research approach to understand students' experiences and perceptions of DD. We asked students to respond to open-ended survey questions regarding DD at two time points and conducted semi-structured follow-up interviews. All data were iteratively open-coded using content analysis. Students' perceptions of DD were lasting and generally positive, including self-reported themes related to DD promoting their awareness of the “real-world applications of science,” and increased “scientific literacy.” Negative perceptions of DD were largely related to issues with “group dynamics.” We detected differences between majors' and nonmajors' perceptions of DD, including in regard to scientific literacy and class time use. DD is a replicable pedagogy that can assist in instilling democratic skills in biology students.