Flourensia cernua DC (Hojasén), Jatropha dioica Sessé (Sangre de Drago) and Lippia graveolens Kunth (Oregano) are three of the main medicinal plants native to the semi-arid regions of northern Mexico. Adaptation to these environments influences their compositional profile and biological activities; however such aspects remain underexplored. Hence this study aimed to compare the proximate composition, antioxidant activity and FT-IR fingerprints of these species collected from different semi-arid regions. The results revealed significant differences (p < 0.05) among collection sites. Overall, samples from San Jerónimo (SJ) and Estanque de León (EL) locations showed higher dry matter, crude protein and nitrogen-free extract contents. Conversely, samples from La Tortuga (T) location exhibited higher moisture, ash, crude fat and crude fibre contents. Regarding antioxidant activity, samples from SJ and EL recorded lower IC50 values in both DPPH• and ABTS•+ assays along with higher FRAP values. Finally, all locations exhibited comparable FT-IR spectra, confirming the presence of several functional groups such as C=O, C–H, C–O, C-N, and N–H. Although variability was site-dependent, we highlight the nutritional and functional potential of F. cernua, J. dioica, and L. graveolens for future applications.