Tropical montane cloud forests (TMCF) under natural disturbances have shown high endemism in early successional vegetation. However, little is known about anthropogenic disturbances and plant endemism in TMCF under ancient agricultural management. In this sense, I assessed the number of species, abundance, and frequency of endemic vascular plants in temporary plots of cultivated and young fallow areas from two maize-based systems: milpa shifting cultivation (MS) and semi-permanent cropping (SP) in Oaxaca, Mexico. Overall, both agricultural stages and systems harbored endemic species, seven in total, but most of such species were found in the fallow stage than in the cropping stage, and in the MS system than in the SP system. A single Asteraceae herbaceous endemic species (Melampodium mimulifolium) was commonly recorded in cultivated fields, but almost exclusive to the SP cropping system. Seven species were recorded in fallows, where the narrow-range endemic tree species Clethra integerrima (Clethraceae) was the most abundant and frequent, but almost exclusive to the MS cropping system. In more permanent and intensified agricultural systems within biodiversity hotspots, only ruderal endemic herbaceous species can persist. In contrast, in low intensity managed agricultural systems, like ancient agroforestry, not only can endemic tree species prosper, but also restricted endemic trees can be found. Indigenous agricultural systems in biodiversity hotspots should not be seen as a threat, but rather as complementary areas for endemism conservation.