The fatigue behaviour of single-lap joints bonded with a hyperelastic silane-modified polymer adhesive was investigated under displacement-controlled (DC) and load-controlled (LC) conditions to clarify the influence of loading control mode on the mechanical interpretation of fatigue degradation in flexible adhesive joints. Quasi-static tests, cyclic fatigue experiments, stiffness evolution monitoring, finite element stress analysis and post-fracture surface examination were combined to establish a comprehensive damage framework. Under displacement-controlled fatigue, stiffness degradation exhibited a three-stage evolution consisting of an initial conditioning phase, a stable quasi-linear decay regime and a final unstable propagation stage. In this configuration, normalized stiffness provided a reliable macroscopic indicator of crack growth because the imposed displacement limits structural amplification effects. In contrast, load-controlled fatigue tests showed stabilization followed by a late-stage increase in stiffness. Experimental observations and mechanical analysis demonstrate that this behaviour originates from geometric nonlinearity, secondary bending and stress redistribution rather than intrinsic material hardening. Despite different degradation manifestations, fatigue life curves obtained under LC and DC conditions displayed comparable power-law slopes, indicating similar macroscopic life sensitivity to the applied severity level. However, internal stress evolution and load-transfer mechanisms differed significantly between control modes. The results reveal that loading control mode induces structural amplification effects that modify stiffness evolution during fatigue. Consequently, distinguishing between intrinsic material degradation and structural response is essential for establishing physically meaningful fatigue interpretation and design criteria in hyperelastic adhesive joints. This work demonstrates that stiffness evolution during fatigue may be misinterpreted if the influence of loading control mode is not considered.