This research aimed to evaluate the HPLC-DAD profile of phenolic compounds, their content and antioxidant capacity in hypocotyls extracts of yellow, red and black maca during pre-harvest, harvest and natural post-harvest drying. A significant increase in total phenolic compounds and antioxidant capacity was observed from pre-harvest to natural post-harvest drying in all three ecotypes. During harvest, red maca had the highest concentration of phenolic compounds. HPLC-DAD analysis revealed the prevalence of 11 phenolic compounds, but with different concentrations in each ecotype and in each stage of study, such as six flavanol derivatives (flavan-3-ol), four derivatives of benzoic acid and an o-coumaric acid derivative. Post-harvest drying, under natural conditions, caused a significant loss (yellow maca 89.90%, red maca 82.49% and black maca 66.31%) of phenolic compounds, mainly derived from benzoic and o-coumaric acid, until non-detectable limits, only two flavanol derivatives (flavan-3-ol) tolerated these conditions. The results of the study suggest improving cultivation techniques and post-harvest management to preserve the content of phenolic compounds.