I have a Bsc in biotechnology with research experience in organic synthesis and a Msc in medical biotechnology with research experience in immunology and a publication.

My Bsc was very related to natural sciences, and i felt that my biomedical Msc was not right for me.

So, can i pursue a phd in industrial or environmental biotechnology, like bioprocessing or bioremediation? Or would my Msc and lack of specific practical experience be a problem?

I'm sure you'll be fine changing direction from a MSc to PhD. This wasn't a problem for me.