Pepper (Capsicumspp.) is among the oldest and most cultivated crops on the planet. Its fruits are widely used as natural condiments in the food industry for their color, flavor, and pungency properties. Peppers have abundant production; on the other hand, their fruits are perishable, deteriorating within a few days after harvesting. Therefore, they need adequate conservation methods to increase their useful life. This study aimed to mathematically model the drying kinetics of smelling peppers (Capsicum chinense) and pout peppers (Capsicum chinenseJacq.) to obtain the thermodynamic properties involved in the process and to determine the influence of drying on the proximal composition of these peppers. Whole peppers, containing the seeds, were dried in an oven with forced air circulation, at temperatures of 50, 60, 70, and 80 °C, with an air speed of 1.0 m/s. Ten models were adjusted to the experimental data, but the Midilli model was the one that provided the best values of coefficient of determination and lowest values of the mean squared deviation and chi-square value in most of the temperatures under study. The effective diffusivities were well represented by an Arrhenius equation, appearing in the order of 10−10m2·s−1for both materials under study, since the activation energy of the smelling pepper was 31.01 kJ·mol−1and was 30.11 kJ·mol−1in the pout pepper, respectively. Thermodynamic properties in both processes of drying the peppers pointed to a non-spontaneous process, with positive values of enthalpy and Gibbs free energy and negative values of entropy. Regarding the influence of drying on the proximal composition, it was observed that, with the increase in temperature, there was a decrease in the water content and the concentration of macronutrients (lipids, proteins, and carbohydrates), providing an increase in the energy value. The powders obtained in the study were presented as an alternative for the technological and industrial use of peppers, favoring obtaining a new condiment, rich in bioactives, providing the market with a new option of powdered product that can be consumed directly and even adopted by the industry as a raw material in the preparation of mixed seasonings and in the formulation of various food products.