Biofertilizer production and application for sustainable agriculture is already a reality. The methods for biofertilizers delivery in crop fields are diverse. Although foliar spray is gaining wide acceptance, little is known about the influence that the biochemical features of leaves have on the microbial colonization. Arthrobacter agilis UMCV2 is a rhizospheric and endophytic bacteria that promotes plant growth and health. In this study, we determined the capacity of the UMCV2 strain to colonize different leaves from Medicago truncatula in a foliar inoculation system. By using two powerful analytical methods based on mass spectrometry, we determined the chemical profile of the leaves in 15-d old plants. The metabolic signatures between the unifoliate leaf (m1) and the metameric units developing above (m2 and m3) were different, and interestingly, the highest colony forming units (CFU) was found in m1. The occurrence of the endophyte strongly affects the sugar composition in m1 and m2 leaves. Our results suggest that A. agilis UMCV2 colonize the leaves under a foliar inoculation system independently of the phenological age of the leaf and it is capable of modulating the carbohydrate metabolism without affecting the rest of the metabolome.