Black carbon (BC) is a major component of submicron particulate matter (PM), with significant health and climate impacts. Many cities in emerging countries lack comprehensive knowledge about BC emissions and exposure levels. This study investigates BC concentration levels, identifies its emission sources, and characterizes the optical properties of BC at urban background sites of the two largest high-altitude Bolivian cities: La Paz (LP) (3600 m above sea level) and El Alto (EA) (4050 m a.s.l.), where atmospheric oxygen levels and intense radiation may affect BC production. The study relies on concurrent measurements of equivalent black carbon (eBC), elemental carbon (EC), and refractory black carbon (rBC) and their comparison with analogous data collected at the nearby Chacaltaya Global Atmosphere Watch Station (5240 m a.s.l). The performance of two independent source apportionment techniques was compared: a bilinear model and a least-squares multilinear regression (MLR). Maximum eBC concentrations were observed during the local dry season (LP: eBC = 1.5 ± 1.6 µg m−3; EA: 1.9 ± 2.0 µg m−3). While eBC concentrations are lower at the mountain station, daily transport from urban areas is evident. Average mass absorption cross sections of 6.6–8.2 m2 g−1 were found in the urban area at 637 nm. Both source apportionment methods exhibited a reasonable level of agreement in the contribution of biomass burning (BB) to absorption. The MLR method allowed the estimation of the contribution and the source-specific optical properties for multiple sources, including open waste burning.