In this paper, we present a structural and optical study on micro-pixelated InGaP/AlGaInP quantum well structures with different pixel sizes down to 6 μm and a red emission at 636 nm. Temperature-dependent photoluminescence and cathodoluminescence cartographies were coupled to observe the emission homogeneity at the pixel scale and to study the impact of non-radiative recombination from sidewall defects. We deduced that micro-LEDs are impacted by surface recombination and we estimated the thermal quenching of photoluminescence related to defects. At low temperatures, a stronger luminescence was also observed from the pixel edges due to the diffusion coefficient or a geometric effect. Finally, the study was completed by a TOF-SIMS analysis in order to provide information about material composition homogeneity.