Peptides are molecular tools for study in different fields of health such as biochemistry, physiology and pharmacology. To obtain them, chemical synthesis coupled to microwaves is carried out and this microwave radiation is key for the coupling of amino acids in the assembly of the peptide. Keeping temperature and exposure times under control is a great challenge in this process. For this purpose, an electronic control was developed in the microwave oven. The microwave oven was modified to adapt it to the process, as a control and data acquisition system, an Arduino UNO card is used, which is responsible for recording the temperature of the sample and sends the signal to enable and disable the microwave power source (Magnetron). To control the temperature, an infrared sensor is used which is responsible for feedback the system and maintain the temperature of the sample at the desired levels.