Background <p>Controlling vegetative vigour is a key part of modern high-density apple orchards that use semi-dwarf rootstocks like M7. Genetic dwarfing is widely employed; however, additional management through chemical growth retardants or physical constraints is frequently necessary to preserve optimal canopy architecture. It is still not clear if these two different approaches stop growth by using the same metabolic pathways or different stress-mediated mechanisms. The objective of this study was to elucidate the physiological, metabolic, and hormonal profiles in three-year-old M7 apple trees exposed to three different treatments: mechanical dwarfing (bonsai techniques), chemical dwarfing (paclobutrazol/PBZ), and untreated controls.</p> Results <p>Even though the two treatments used different methods, they both worked to keep shoot elongation to less than 12% of the control. Hormonal regulation was the main cause of PBZ-induced dwarfing. This was shown by a marked decline in gibberellin A3 (GA3; 63% drop) and a rise in zeatin. This change in hormones was significant starch accumulation and better absorption of macronutrients with few signs of stress. In contrast, dwarfing through bonsai techniques caused a systemic stress response, as shown by a 284% rise in the stress osmolyte sorbitol and a 190% rise in abscisic acid (ABA). This group also had low nutrient levels, a sharp drop in the GA/ABA ratio, and clear signs of physiological stress, like lower photosynthetic efficiency and higher oxidative markers.</p> Conclusions <p>Our results show that PBZ acts as a precise biochemical regulator that produces a sink-limited state without imposing substantial physiological stress on the plant, whereas bonsai techniques control growth by causing a resource-limited, stress-driven physiology. These contrasting signatures highlight paclobutrazol as a more controlled dwarfing tool and provide a physiological framework for developing stress-resilient dwarfing rootstocks.</p>