Estimated climate change scenarios demand robust coffee cultivars tolerant to supra-optimal temperatures, water deficit, diseases, and other stresses. Wild Coffea species represent important genetic resources for resilience. The study of variations in morphological structures associated with transpiration control, such as stomata, represents an important approach for identifying genotypes with greater stress tolerance. This study evaluated stomatal density and morphology in 48 wild accessions, 24 of Coffea racemosa and 24 of C. zanguebariae, from provinces of Mozambique. Leaf samples provided microscopic images to assess stomatal traits: density (SD), polar diameter (PD), equatorial diameter (ED), stomatal functionality (SF), and leaf dry mass. Principal components were analyzed for all 48 accessions and separately by species. Mean distribution independence was tested with the Mann–Whitney test (p < 0.05). Results revealed inter- and intraspecific variation. The ability to distinguish accessions varies with the set of traits and species. A significant negative correlation between ED and SF was shared by both species, suggesting a conserved functional pattern. This study discusses the differences in stomatal traits between wild and commercial coffee species and aspects related to possible alterations of stomatal structures during their adaptation to climate change. Additionally, it points to accessions with potential use in genetic breeding programs to increase stomatal function and the possible adaptation of new cultivars.