Though land use change has been shown to have great influence on soil structure and C storage, little is still known how these effects change over the long term, especially in Africa. Thus, a study was conducted in central highlands of Kenya to evaluate changes in soil aggregates and aggregate-associated C content across four land use types. The four land use types included (1) an undisturbed bush land, (2) over 50 years old grazed pasture, (3) over 80 years old coffee plantation, and (4) a maize field cultivated continuously for 3 years. It was hypothesized that soil aggregates and aggregate-associated C would decrease with increasing soil disturbance caused by tillage or exerted by livestock hooves, with the magnitude of these effects being reduced by abundance of earthworms and termites. Land use type significantly affected soil aggregates especially, large macroaggregates and microaggregates. The weight of large macroaggregates in bush land (14.4 g 100 g−1 soil) was more than 20 times higher than in maize field (0.6 g 100 g−1). On the contrary, the weight of microaggregates in maize field (41.2 g 100 g−1) was more than double that recorded in bush land (18.8 g 100 g−1). Aggregate-associated C showed magnitude of differences similar to those of soil aggregates. However, the abundance of earthworms and termites generally showed weak or no correlation with soil aggregate fractions and aggregate-associated C. Our results shows that land use change can significantly influence soil aggregation and C content, which could have far-reaching implications for the long term C sequestration.