In this study, we characterize atmospheric ozone over the tropical Andes in the boundary layer, the free troposphere, and the stratosphere; we quantify each contribution to total column ozone, and we evaluate the performance of the multi-sensor reanalysis (MSR2) in the region. Thus, we present data taken in Ecuador and Peru (2014–2019). The contribution from the surface was determined by integrating ozone concentrations measured in Quito and Cuenca (Ecuador) up to boundary layer height. In addition, tropospheric and stratospheric column ozone were quantified from ozone soundings (38) launched from Quito during the study time period. Profiles were compared against soundings at Natal (SHADOZ network) for being the closest observational reference with sufficient data in 2014–2019. Data were also compared against stratospheric mixing ratios from the Aura Microwave Limb Sounder (Aura MLS). Findings demonstrate that the stratospheric component of total column ozone over the Andes (225.2 ± 8.9 Dobson Units [DU]) is at similar levels as those observed at Natal (223.3 ± 8.6 DU), and observations are comparable to Aura MLS data. In contrast, the tropospheric contribution is lower over the Andes (20.2 ± 4.3 DU) when compared to Natal (35.4 ± 6.4 DU) due to a less deep and cleaner troposphere. From sounding extrapolation of Quito profiles down to sea level, we determined that altitude deducts about 5–7 DU from the total column, which coincides with a 3%–4% overestimation of the MSR2 over Quito and Marcapomacocha (Peru). In addition, when MSR2 data are compared along a transect that crosses from the Amazon over Quito, the Ecuadorian coast side, and into the Pacific, observations are not significantly different among the three first locations. Results point to coarse reanalysis resolution not being suitable to resolve the formidable altitude transition imposed by the Andes mountain chain. This work advances our knowledge of atmospheric ozone over the study region and provides a robust time series of upper air measurements for future evaluations of satellite and reanalysis products.