Characteristics developed by Cactaceae for adaptation to climates where water is limited include crassulacean acid metabolism (CAM), a thick cuticle, and spines and trichomes that intercept a proportion of solar radiation. A few studies consider morpho-anatomical and physiological characteristics of Cactaceae seedlings, which may help understand their establishment, growth, and eventual reproduction. In this study, photosynthetic metabolism (titratable protons) and morpho-anatomical features of Stenocereus beneckei seedlings were examined under limiting water conditions. Soil moisture treatments consisted of -0.03, -0.5, -1.5, and -3.0 MPa, and seedling samples were taken at 3 h intervals on one day at 7 and 9 months of age with three replicates per treatment. The results show irregular fluctuations in acidity concentrations during the first 6 and 7 months of age; at 9 months, an increase in titratable proton values was observed during the night, and it seems that soil moisture does not determine CAM expression. Seedlings from smaller seeds are less tolerant to water stress, they had poor growth in all treatments, and at -3.0 MPa after 3 months of drought none survived. Anatomical observations show collapsed cells associated with a high accumulation of calcium oxalate crystals and starch grains, as a response to water deficit. Titratable acidity concentration increased with seedling age, and CAM expression did not accelerate with soil water deficit.