Background: Antimicrobial resistance (AMR) is a growing global public health threat, and effective treatment of microbiological waste is essential in preventing the spread of resistance genes into the environment. Autoclaving is commonly used in healthcare and laboratory settings to sterilize microbiological waste, ensuring the destruction of viable bacteria. However, the fate of antimicrobial resistance genes (ARGs), such as blaCTX-M and blaTEM, following autoclaving is not well understood. To fill this critical gap, this study determined the PCR stability of AMR encoding genes from autoclaved microbiological waste in Mwanza, Tanzania. Methods: A laboratory-based experimental study was conducted between May and August 2024 at the Catholic University of Health and Allied Sciences (CUHAS). Standard and resistant E. coli strains carrying blaCTX-M and blaTEM genes were subjected to autoclaving at 121°C and 0.1 MPa for varying duration. Bacterial viability was assessed through sub-culturing on MacConkey agar, while the presence of ARGs was evaluated using multiplex PCR.