Solving the world food problem, health, and sustainability issues have become principal objectives of modern biotechnology. With the help of genetic engineering, the DNA of micro-organisms can be altered to produce value-added products (e.g., enzymes, vitamins, and alternative proteins) efficiently and sustainably. There has been lots of research activity about public perception and acceptance of genetic engineering in the food industry during the last decades. The EU Regulations provide significant loopholes, and companies fear strong anti-genetically modified organisms (GMO) lobby due to early scandals to notably GMO plants and animals. Until now, most research groups studied the public perception of genetically modified animals (GMAs) and genetically modified plants (GMPs). However, the public perception towards genetically modified micro-organisms (GMMs) has not been studied intensively, while valuable products are hampered. This research explores public emotions and underlying ethical concerns towards GMMs in the dairy-based industry through literature research, semi-structured expert interviews, and online questionnaires. Experts in this field hypothesize that people look differently towards specific GMO products and that consumer acceptance rises when a clear benefit is given. Techno-ethical scenarios were created to study laypeople and to verify different propositions made by experts. Roeser (2018) argues that moral emotions can play an important role in judging the ethical aspects of risky technologies. We used the theoretical approach from Roeser (2018) as a guideline to offer concrete recommendations for further study and essential elements to consider for decision-making on GMM technology. From this research, it can be concluded that the opinions, as in other debates, do not seem to be polarized. The majority of the public feels optimistic about GMM products when it gives a clear benefit. The emotions point to ethical concerns that are most important for specific types of products and consumers. The negative emotions (fear, anger, powerlessness, irritation, and disgust) and positive emotions (interest, hope, joy, happiness, and surprise) link to awareness, trustworthiness, and autonomy to be essential for GMM product acceptance.