The Peruvian carrot is a root that is rich in bioactive compounds. However, owing to the short shelf life of these carrots, their consumption is restricted. In the present study, we investigated the microwave vacuum drying (MWVD) of restructured Peruvian carrot chips. Two microwave power levels, namely, constant and two-stage, were considered and evaluated to determine their relationship with drying time, kinetic parameters, energy consumption, and preservation of carotenoids and phenolic compounds. At the constant microwave power level, drying time decreased with increasing drying rate, sample temperature, and energy consumption. However, it did not affect the drying rate at the end of the drying. At the two-stage microwave power level, the drying time was similar to that observed in constant power level experiments. However, sample temperature and energy consumption were decreased when drying at a lower power level. Nutritional compounds were better preserved by using the highest tested power level at the two-stage level and the lowest tested one at the one-stage power level. Page’s and Fick’s models presented an excellent fit of the experimental data. Using the two-stage microwave power level at a higher initial power level (MWVD-5-1) saved energy, decreased the drying duration, and preserved the bioactive molecules in restructured chips.