The aim of the EU project LikeMeat was to develop a novel extruded meat analogue. To assess the hygiene and safety status of the products, nine different proteins, derived from plants, milk and egg, were analyzed before and after the cooking extrusion process. In detail, the following microbial criteria were analyzed: total aerobic mesophilic count, psychrotrophic count, Enterobacteriaceae, Coliforms, Coagulase-positive staphylococci, bacilli with the main focus on B. cereus, Pseudomonas aeruginosa, Clostridium with the main focus on Clostridium perfringens, Listeria spp., Salmonella spp. and yeast/mold counts. The results of the protein powders showed variable levels of potential food spoilage microbes and endospore-forming bacteria, but no human pathogens were detected. After the cooking extrusion of different protein mixtures the microbial load of the products was analyzed. The results displayed that bacterial endospore formers are able to survive the applied cooking extrusion process.