The M.Sc. Microbiology program was established in 2007 at Himachal Pradesh University under the Self Financing Scheme in the Department of Biotechnology. However, in order to strengthen the discipline and as a result of the necessity felt especially during Covid Pandemic, a separate independent department of Microbiology was created under the Faculty of Life Sciences which started functioning in 2020.Thereafter in 2022, the university also started the Ph.D. program along with Masters (M.Sc. Microbiology) program. The Department is located on the ground floor of a 4 storied Multi Faculty Phase I building.

A common entrance test is conducted for the admission to M.Sc. Microbiology program by Himachal Pradesh University (Main Campus), Central Research Institute (CRI) Kasauli and Shoolini Institute of Life Sciences and Business Management (SILB). On the basis of entrance merit and preference of student the seats are allotted. There are 30 seats in HPU Main campus, out of which 15 are subsidized and 15 are non-subsidized while  one seat each for Sports person, Physically challenged and two seats for Single Girl Child and 3 for Economically Weaker Section are also available, 15 seats available in CRI Kasauli out of which 8 are subsidized and 7 are non-subsidized and 2 seats for in-service candidates and three for the wards of CRI/HPU employees are also available through entrance test, SILB has 30 non-subsidized seats. For PhD in Microbiology the students having valid JRF score can apply in June/July cycle in response to the advertisement issued by the University and shortlisted candidates have to appear for interview. The university also conducts a separate entrance test for the vacant seats of Ph.D. program for Non JRF students in  December/January cycle.

The department is now well-established, with permanent faculty members and also guest faculty. The Department has well-equipped laboratories with the necessary instruments to carry out research. The departmental Central Instrumentation Facility houses several high-end equipment.   Besides this the facilities of University Scientific Instrumentation Centre (USIC) and Biotechnology Incubation Centre (BIC) supported by the Department of Industries, Govt. of Himachal Pradesh through HPSEDC and also HP University are available for the students. Department faculty members have published numerous research and review papers in peer-reviewed journals of international repute.

The students of the Microbiology Department are a vibrant group, enthusiastically organizing and participating in various activities of the department, such as the Annual Sports Day, Monthly Journal Club, Monthly Work presentations, quiz competitions, lecture series, and field trips.

The Department of Microbiology at H.P. University brings together all the faculties with specialization in different Microbiology domains to enhance the knowledge of students in diverse fields of Microbiology. The main thrust areas of the Department are Microbial Enzymes, Bioprocess development for synthesis of industrially important products, Medicinal plants and therapeutics, Medical Microbiology, Parasitology, Immunology, Environmental Microbiology, Antimicrobial drug resistance, Virology, and Molecular Biology.