The effect of temperature and drying systems on mucilage and cellulose (obtained by the microwave-assisted extraction technique, MAE) from Opuntia ficus-indica (OFI) and Austrocylindropuntia cylindrica (CC), was determined, using a conventional oven (CO) and Refractance window (RW). Mathematical modeling was performed from drying kinetics data using Lewis, Henderson Pabis, Page, and logarithmic models. Activation energy (Ea) and diffusivity (D) were also determined. The model with the best fit was the logarithmic one, with a correlation coefficient (R2) greater than 0.99. The obtained activation energies were 22.81 kj mol-1 for Refractance window (RW) and 31.44 KJ mol -1 using conventional hot air drying (CO) while a diffusivity of 2.9 *10-8 m2 s-1 for RW and 1.3*10-8 m2 s-1 for CO were found as well. According to our results, a greater drying efficiency and a less chemical deterioration of the plant sample are obtained when they are dried using Refractance window.