M.Sc Eligibility

Yes, you could choose between any life science courses you want. Assuming you have two reasons to change field:-
1. Thinking that no job opportunities for a Bachelor degree and/or for microbiology
2. Recently developed an interest in food technology, so you could pursue Ph.D or get a dream job in the same domain (or you decided to join with friends pursuing food technology).
However, if you still have interest in microbiology, there are definitely varied opportunities for microbiologists. Instead of doing M.Sc, you could do a job oriented Diploma course like certificate program in quality control microbiology, one such course is offered by the big player pharma company based in Bangalore.
Once after securing job and gaining few yrs of experience, where you have real experience to learn not just food tech but also about other career opportunities. Also to interact and learn from the scientists and team members. Well, you could take a call that time. You could quit job to follow your dream, of if you decided to do Ph.D, many companies like Biocon, Dr Reddy's offer research program for the employees.
Good luck!