Komagataella phaffii has become a key player in biotechnology used for the production of heterologous proteins with numerous GRAS notices and QPS status released in the past years. While most of these descriptions and scientific studies focus on strain engineering, products and cultivation processes, this paper provides fundamental data about the general viability of K. phaffii after post-production biomass treatments and co-incubations with non-sterile soil and water samples. A comparison of different K. phaffii strains uncovered a high thermal sensitivity for all tested strains, which was further enhanced under alkaline conditions. A rapid reduction in the viable cell number started at approx. 52 °C and terminated in a full loss of 109 viable cells per milliliter within seconds at 70 °C. Survival rates of untreated non-GMO and GMO K. phaffii strains in water- and soil-slurry-microcosms demonstrated that the number of viable K. phaffii cells decreased rapidly and comparably to a Saccharomyces cerevisiae reference. No mating events were detected under these environmental conditions. These findings supported assumptions that K. phaffii is highly specialized and not a ubiquitous microorganism as described for other yeasts. Finally, intrigued by the low survival outside optimal laboratory conditions, K. phaffii biomass was evaluated in mesophilic anaerobic digestion processes for energy production. Enhanced methane yields and a concomitant loss of viable K. phaffii cells were demonstrated.