Glucosinolate profiles, glucosinolate contents and myrosinase activity were evaluated in yellow, red and black hypocotyls of maca during pre-harvest, at harvest and during post-harvest drying. At harvest, six glucosinolates (GLs) were identified: 5-methylsulfinylpentyl, 4-hydroxybenzyl, benzyl, 3-methoxybenzyl, 4-hydroxy-3-indolylmethyl and 4-methoxy-3-indolylmethyl, of which benzyl glucosinolate was the most abundant in the three ecotypes, representing 80% of the total GLs. A significant increase in GLs was observed for the three ecotypes during the 90 days before harvest and during the 15-30 days of post-harvest drying. This was followed by an important decrease of GLs during the 30-45 day period, which was attributed to cell breakdown, due to fluctuations in temperatures during the drying process, and was correlated with a high myrosinase action. During the last period of post-harvest drying, GLs were much lower and correlated to lower myrosinase activity and lower maca hypocotyl humidity. A combination of artisanal and other processing techniques should be utilised, in order to best preserve maca glucosinolates.