Soil macrofauna such as earthworms and termites are involved in key ecosystem functions and thus considered important for sustainable intensification of crop production. However, their contribution to tropical soil and crop performance, as well as relations with agricultural management (e.g. Conservation Agriculture), are not well understood. This study aimed to quantify soil macrofauna and its impact on soil aggregation, soil carbon and crop yields in a maize-soybean system under tropical sub-humid conditions. A field trial was established in Western Kenya in 2003 with tillage and residue retention as independent factors. A macrofauna exclusion experiment was superimposed in 2005 through regular insecticide applications, and measurements were taken from 2005 to 2012. Termites were the most abundant macrofauna group comprising 61% of total macrofauna numbers followed by ants (20%), while few earthworms were present (5%). Insecticide application significantly reduced termites (by 86 and 62%) and earthworms (by 100 and 88%) at 0-15 and 15-30 cm soil depth respectively. Termite diversity was low, with all species belonging to the family of Macrotermitinae which feed on wood, leaf litter and dead/dry grass. Seven years of macrofauna exclusion did not affect soil aggregation or carbon contents, which might be explained by the low residue retention and the nesting and feeding behavior of the dominant termites present. Macrofauna exclusion resulted in 34% higher maize grain yield and 22% higher soybean grain yield, indicating that pest damage – probably including termites - overruled any potentially beneficial impact of soil macrofauna. Results contrast with previous studies on the effects of termites on plant growth, which were mostly conducted in (semi-) arid regions. Future research should contribute to sustainable management strategies that reduce detrimental impact due to dominance of potential pest species while conserving soil macrofauna diversity and their beneficial functions in agroecosystems.