Climate change affects plant acclimation and adaptation, particularly in long-lived perennial crops like apple (Malus domestica Borkh.). Stomata play an essential role in regulating these plant environmental responses. This study examined variation in stomatal density (SD) and stomatal function of apple trees in 2022–2023 across four European locations (Spain, ESP; France, FRA; Italy, ITA; and Switzerland, CHE, the only non-irrigated orchard). A total of 20 preselected apple accessions with extreme SD phenotypes (HSD and LSD) and five commercial varieties (MSD- Comm) were compared. Across locations, SD was consistent for each SD group, but partial plasticity emerged under heat stress in ESP and FRA. In ESP, SD increased under high temperatures and irrigation, but the increase was only significant for MSD- Comm (p < 0.05). In FRA, HSD decreased under high temperatures and limited irrigation in 2022, but these changes reversed under wetter conditions in 2023 (p < 0.05), reinforcing SD stability and the capacity for local acclimation. Net carbon assimilation (Anet) showed no significant differences across SD groups and locations. Stomatal conductance (gs) adjusted to local climate and produced variations in intrinsic water-use efficiency (iWUE). Conditions in FRA, ITA, and CHE also led to a significant correlation between integrated WUE (δ13C) and Total Fruit Weight (p < 0.01, R2 = 0.20). In contrast, high temperatures and irrigation in ESP maintained no correlation between δ13C and Total Fruit Weight. These results highlight the role of SD in short-term acclimation and, given its stability across environments, great potential for breeding climate-adapted apples.