Active methodologies for teaching propose tools and strategies for improving student learning by using participative and integrative approaches. These lead students to autonomous research for industry problems and solutions. This study aimed to apply active-project active methodologies to undergraduate soil microbiology and inoculant courses to verify students' perception of their knowledge levels on these topics. Forty undergraduate students received the traditional methodology that presented theoretical contents referring to the soil microbiology and inoculants; one group of twenty also elected to receive active methodologies based instruction during which they developed active projects that were structured in seven steps: briefing, bibliographic research, problematization and resolution, solutions, abstract and banner creation, and presentation. At the end of the academic year, all students answered a questionnaire to verify the perception of their levels of knowledge of soil microbiology and inoculants. Regarding the topic of microbial inoculants, perceived knowledge was the same for both groups, but overall, the active methodologies group had higher perceived knowledge of good practices of inoculation. The two groups were clustered by a multivariate approach, confirming that the use of active projects can increase the knowledge and level of subject matter understanding. The active projects contributed to undergraduate students' increased assimilation and perceived understanding of soil microbiology subject matter content and microbial inoculant issues. The active projects can be explored in other subdivisions of soil science, including agriculture and environmental studies. Keywords Undergraduate students. Agricultural and biology education. Soil microbiology education. Participative and integrative learning Highlights • Use of active-project increases the level of students' knowledge about soil microbiology. • Active of teaching approach could be universal for soil sciences and related sciences. • Active-projects are emergent tools to better knowledge soil microbial applications.