This study examines the carbonaceous-aerosol characteristics at three contrasting urban environments in Greece (Ioannina, Athens, and Heraklion), on the basis of 12 h sampling during winter (January to February 2013), aiming to explore the inter-site differences in atmospheric composition and carbonaceous-aerosol characteristics and sources. The winter-average organic carbon (OC) and elemental carbon (EC) concentrations in Ioannina were found to be 28.50 and 4.33 µg m−3, respectively, much higher than those in Heraklion (3.86 µg m−3 for OC and 2.29 µg m−3 for EC) and Athens (7.63 µg m−3 for OC and 2.44 µg m−3 for EC). The winter OC/EC ratio in Ioannina (6.53) was found to be almost three times that in Heraklion (2.03), indicating a larger impact of wood combustion, especially during the night, whereas in Heraklion, emissions from biomass burning were found to be less intense. Estimations of primary and secondary organic carbon (POC and SOC) using the EC-tracer method, and specifically its minimum R-squared (MRS) variant, revealed large differences between the sites, with a prevalence of POC (67–80%) in Ioannina and Athens and with a larger SOC fraction (53%) in Heraklion. SOC estimates were also obtained using the 5% and 25% percentiles of the OC/EC data to determine the (OC/EC)pri, leading to results contrasting to the MRS approach in Ioannina (70–74% for SOC). Although the MRS method provides generally more robust results, it may significantly underestimate SOC levels in environments highly burdened by biomass burning, as the fast-oxidized semi-volatile OC associated with combustion sources is classified in POC. Further analysis in Athens revealed that the difference in SOC estimates between the 5% percentile and MRS methods coincided with the semi-volatile oxygenated organic aerosol as quantified by aerosol mass spectrometry. Finally, the OC/Kbb+ ratio was used as tracer for decomposition of the POC into fossil-fuel and biomass-burning components, indicating the prevalence of biomass-burning POC, especially in Ioannina (77%).