This work evaluates the applicability of the reference protocol EUSAAR2 in the Semi-Continuous OCEC analyzer under two environments, an urban background site influenced by traffic emissions and a regional background site. The comparison of the 24-h averaged OC and EC measurements of the Semi-Continuous analyzer with the OC and EC concentrations determined offline in PM2.5 24 h filters yielded very good agreement for both denuded and undenuded samples. In the urban background site, the regression for EC yielded a slope of 0.93 and 1.04 (b = 0.07 and 0.05, R2 = 0.83 and 0.84), for denuded and undenuded samples respectively. The slopes of OC regressions were 0.99 (b = −0.18, R2 = 0.81) for the low volume and 0.93 (b = 0.12, R2 = 0.84) for the high volume samples. In the regional background site, the slopes of the EC regression with the denuded and undenuded samples was 0.91 and 1.02 correspondingly (b = 0 and − 0.03, R2 = 0.77 and 0.89). The regression of OC had slopes close to 1; 1.03 for the high volume and 0.95 for the low volume sampler (b = 0.08 and 0.26, R2 = 0.78 and 0.78). BC measurements obtained by an aethalometer and MAAP were in very good agreement with EC at both sampling sites. BC levels were consistently higher than EC (slope of the regression aethalometer BC vs EC slope a = 1.2, intercept b = 0.19, R2 = 0.79, for the urban background site and a = 1.9, b = −0.04, R2 = 0.94, for the regional site, slope MAAP BC vs EC a = 1.2, b = 0.06, R2 = 0.94, for the urban background site and 1.7, b = −0.03, R2 = 0.96, for the regional site). This confirms the need of using the site-specific mass absorption cross section (MAC) instead of the ones provided by manufacturers for the conversion of absorption units into BC mass concentration. BC data correlated very well with the optical EC obtained from the semi-continuous OCEC analyzer (a = 1.3, b = 0.16, R2 = 0.80 for the urban background site and a = 1.7, b = 0.009, R2 = 0.94 for the regional site, respectively). The comparison of OC concentrations by the Semi-Continuous Sunset analyzer with organic aerosol online measurements by ACSM showed strong correlations. The ratio OA/OC was 1.9 and 2.3 for the urban background and regional sites. The accumulation of refractory material on the filter, because of prolonged periods of sampling, caused a shift of the split point to the inert mode and changes on PC formation and evolution. Extreme dust outbreaks lead to the overestimation of OC due to the evolution of carbonate in the He mode. Generally, the Sunset Semi-Continuous OCEC analyzer with EUSAAR2 provided robust and consistent measurements with offline thermal-optical analysis.