This study focuses on enhancing the catalytic properties of copper-modified MOF235 (Cu-MOF235) in the wet-oxidation for methylene blue (MB) removal from aqueous solutions, while also optimizing process conditions. The impact of variables such as catalyst dosage (0.005–0.02 g), pH (4–10), temperature (20–40°C), reaction time (5–60 min), and catalyst type on dye removal is investigated. The SEM, EDX, FTIR, and XRD techniques were used to investigate the structural and physical characteristics of the synthesized catalyst. The statistical approach of Design of Experiments (DOE) systematically establishes the relationship between process factors and output. Increasing catalyst dosage boosts active sites for faster degradation or transformation of dye compounds, although diminishing returns may arise. Elevated temperatures reduce activation energy, increasing the MB removal rate. Cu-MOF235 surpasses MOF235 due to enhanced active sites, robust chemical interactions, surface modifications, potential synergies, catalytic degradation, and altered solution chemistry. The degradation of MB in the presence of Cu-MOF235 and aeration can proceed through a series of steps by adsorption, activation of oxygen, catalytic degradation, formation of intermediate products, complete degradation, and desorption. This research underscores the significant impact of catalyst modification on dye removal and offers insights into optimizing such processes.