<p>In the Colombian Amazon, the loss of vegetation cover is a critical threat to the diversity of soil macrofauna and the provision of soil ecosystem services (SES). This study aims to evaluate how cocoa agroforestry systems (AFS) in the northwestern Colombian Amazon impact the synergy between soil macrofauna and SES under four land-use change systems: A typical tropical rainforest (Forest), two AFS established after natural regeneration (AFS1-Reg) and pasture (AFS2-Pas), and a traditional grazing system (Pasture). In each system, soil samples were collected from six replicates per land-use to analyze soil macrofauna taxa, soil physical and biochemical properties. Physical and biochemical properties were integrated into five different SES: (i) support for plant growth, (ii) soil aggregation, (iii) soil erosion control, (iv) soil carbon storage and (v) nutrient availability, which were used to estimate the Soil Quality Index (SQI). In addition, the abundance of twelve key soil macrofauna taxa was integrated to estimate a Soil Macrofauna Index (SMI). The results showed that land-use change for Pasture system establishment resulted in a loss of key macrofauna taxa and the capacity to provide SES, conversely, AFS improved the provision of SES and the recovery of key macrofauna taxa. The SQI showed a positive correlation with SMI (0.598), and in both indices, AFS implementation showed increasing scores by 23% and 38%, respectively, compared to Pasture system, highlighting the importance of soil macrofauna in the regulation of SES and the need to revise management strategies focused on mitigating the impacts of land-use change, particularly for traditional pasture establishment, which directly alters soil properties and macrofauna essential to ecosystem service regulation.</p>