In this study, the three most known varieties of the Peruvian Maca (Lepidium meyenii), yellow, red, and black, were fractionated in multiple sub-samples and submitted to heating (from 25 to 200 °C) during one hour at 10-minute intervals to be measured using the near-infrared (NIR) spectroscopy after 24 h resting in a desiccator. The study focused on changes related to heating for considering new applications on Maca-enriched food products such as bread, cakes, and cookies, which are prepared over high temperatures during different time exposures. To perform the experiment, 9 portions of 1 g of each sample remained in an oven at each temperature (25, 50, 100, 150, 160, 170, 180, 190, and 200 °C) for different times (10, 20, 30, 40, 50, and 60 min). The principal component analysis (PCA) and the multivariate curve resolution with alternating least squares (MCR-ALS) were applied to interpret the results. In general, it was observed that spectral variations start to occur from heating samples from above 100 °C. The recovered signals indicated that most spectral variations occurred in regions assigned to NH vibrations, suggesting that heating influences the protein and/or macamides structures, which are responsible for most of the properties attributed to the Peruvian Maca. The yellow Maca phenotype was the most susceptible to spectral variations after heating, while the black Maca displayed the slowest spectral transformations. This study may encourage deeper investigations into the use of Maca-derived foods regarding their health-beneficial effects after heating to indicate the limitations of Maca applications.