Single-cell protein (SCP) is a promising alternative for replacing plant and animal-derived dietary proteins. SCP contains essential nutrients and high levels of essential amino acids (AA). Given the versatility of microbial strains and waste substrates that can be used as feedstocks, many variations of production processes can be explored. Improving these microorganism strains by enhancing their properties and productivity is vital to increasing SCP competitiveness. One of the options to enhance microorganism strains would be by creating mutants with better AA profiles. By using mutagenesis and AA inhibitors it should be possible the create novel strains with improved AA-producing properties. The use of AA inhibitors to promote selective pressure on SCP-producing strains is a novel concept and is not a widely explored approach, therefore, the further development of this method should be explored. This paper used a multi-criteria decision analysis method to evaluate different technological factors vital for creating protein-rich mutants. These factors are microorganism strains, agro-industrial waste substrates used as process feedstocks, AA inhibitors, and mutagenesis methods. Microorganisms Candida utilis and Bacillus subtilis showed the highest potential for being used. Molasses was the ‘closest to the ideal’ substrate to be used as feedstock for SCP production. As the most promising mutagenesis method ethyl methane sulphonate was selected. Glufosinate ammonium and methionine sulfoximine for both bacteria and fungi were identified as the best inhibitors for SCP-rich mutant selection. Identified combinations of optimal solutions for microorganisms, substrates, inhibitors, and mutagenesis techniques should be further investigated and evaluated in laboratory settings. This could help to increase SCP's competitiveness as a sustainable protein source.