Agriculture is facing the challenge of increasing the quality of food production with environmentally friendly and health compatible processes featuring limited use of chemicals. The elimination of pathogens and harmful biological agents still remains a fundamental requirement. Therefore, soil physical disinfestation and disinfection represent a promising approach to a sustainable and profitable agriculture. For this reason, a cheap and selective method based on microwave power is proposed. Microwave soil disinfection is based on increasing the soil and, consequently, the pathogens temperature, by radiating the system with microwaves and maintaining the temperature over a threshold value for a sufficient time. This work deals with the nonlinear modeling of electromagnetic and heating phenomena involved in the soil disinfection. Thus, the feasibility of the proposed approach is demonstrated in a realistic case and an optimal design process is derived for any kind of soil.