Should I opt for M.Sc in microbiology or pursue M.Sc in biotechnology after completing B.Sc in biotechnology?

It totally depends on your interest, just choose according to your choice. But there are vast employment opportunities in biotechnology field as they can be absorbed in a number of research institutions, Center for Cellular and Molecular Biology, National Botanical Institute Agricultural Research In

Biotechnology and Microbiology are quite different. Biotechnology is relatively new and has quite good scope. Since you have done B.Sc Biotechnology, you should be familiar with the course. If you didn't like it, then no need to pursue for Masters.

You should go in the same field. So, I think you must go for M.Sc. Biotechnology. As it will benefit you more. And you will be going to get specialization in one field.