Hello there, I am dr.milan an infectious disease specialist answering your question. Yes this can happen, green stool because when amoebiasis is there is cause some pus formation and along with some dietary fat it produces green colour stool. Just make sure that You have been diagnose by a reliable Microbiology lab and by a qualified doctor Microbiologist. Because to diagnose amoebiasis is a somewhat difficult by pathologist now a days. I suggest you to complete the course of drug given by your physician. And just repeat stool microscopy test specially for amoebiasis after completion of drug course. Hope i have given appropriate guidance to you. if you have any query you can consult me anytime. Give me star rating, helpful vote & thank you according to your satisfaction level. Thanking you.