The tubers of Lepidium meyenii (commonly known as maca) have been used in the Andean cuisine for ages. The study aims to determine the behavior of the extract from the red phenotype of maca in the in vitro gastrointestinal tract model and also to define the overall impact of the extract on the microbiota. Glucosinolates, lepidilines, and a deriv- ative of β-carboline alkaloid, i.e. 1-methyltetrahydro-β-5,6-hydride-carboline-3-carboxylic acid, as representatives of one of the main groups of metabolites were selected for the quantitative analysis after in vitro digestion at every stage of the digestion model. The results showed that lepidilines remained highly stable throughout the digestive simula- tion, whereas glucosinolates and the β-carboline derivative were substantially degraded, under the influence of the enzymes and bacteria applied in the “large intestine”. In addition, the red maca extract exhibited prebiotic activity by promoting the growth of selected lactic acid bacteria, with Lactococcus lactis showing the most pronounced response, suggesting that maca-derived preparations may hold promising potential as ingredients in functional foods and microbiota-targeted nutritional formulations.