Studies on soil organic carbon (SOC) storage and stability require the separate assessment of soil fractions in relation to protection against loss. This on-farm study assessed the role of primary (sand, silt, and clay) and secondary (micro- and macroaggregates) particle size fractions on the physical protection of SOC to 30-cm depth of nine agricultural and three forest land uses within three contrasting ecoregions of Costa Rica (i.e., Isthmian-Atlantic moist, Pacific dry, and Montane forest). Specific objectives were to: (1) determine the effect of land use in each ecoregion on particulate organic matter carbon (POM-C), silt plus clay-associated carbon (S+C-C), and micro- and macroaggregate associated water-stable aggregate carbon (WSA-C), and (2) establish the relationships among aggregate properties and SOC concentration. Aggregate stability was characterized by studying the WSA, mean weight diameter (MWD), and tensile strength (TS). Soils under coffee (Coffea arabica), oil palm (Elaeis guineensis), and pineapple (Ananas comosus) plantations had high clay contents to 30-cm depth (ranging between 42.9 and 60.7%), which indicated a high potential for SOC storage. In comparison to less disturbed forest soils, micro- and macroaggregation was not strongly affected by agricultural land use. At coffee and pasture land uses, POM-C concentration was significantly lower (ranging between 0.4 and 2.0 g C kg−1). Between 58 and 98% of SOC was associated with S+C fractions indicating the importance of these particle size fractions to SOC storage. The S+C-C and micro- and macroaggregate-C concentrations differed mainly among pineapple, mango (Mangifera indica), pasture, and other land uses within ecoregions. Further, there was no general tendency of higher C concentrations in the macro- vs. the microaggregate fractions in contrast to the aggregate hierarchy theory. The MWD was affected by land use only for pineapple and organic farming, and it decreased for mango and coffee with increase in soil depth. Correlations among SOC, texture, and TS were site-specific. Silt content was more important than the other particle size fractions in explaining SOC contents. In summary, the amount of physically separated soil fractions and their C storage and stability to 30-cm depth differed mainly among pineapple, mango, pasture, and coffee in specific ecoregions. Well-designed long-term field experiments in Costa Rica are needed to develop management practices for enhancing SOC storage and stabilization in physically separated soil fractions.