Hii!
You can go for msc courses in any of the three subjects you mentioned in the question. But, if you have a specific subject in final year, that is, microbiology, you have a variety of courses to pursue. Some of them are - clinical microbiology, industrial microbiology, medical microbiology, diploma courses, microbial genetics and bioinformatics, applied microbiology etc.,
Hope this helps.
Good luck!

Try pursuing MSc in Chemistry, after BSc in Microbiology, if interested for better career scope and prospects. You may henceforth work in the Industry, Pharmaceutical Companies, CSIR National Research Labs or enter Academia as Faculty. You may even go for a Doctoral degree in future to higher technical institutes like Top IITs, IISc Bangalore and so on.

However, this is my perception, you may even pursue Masters/PhD in Microbiology or Biotechnology, however the career scope and prospects are lesser than Chemistry.