With the scarcity of fresh water and rise in pollution load in the aquatic ecosystem over the globe, the domestic and industrial effluents need to be reused after suitable treatment. In an attempt to do so, soil biofilters have been identified as a treatment alternative that is suitable for application in developing countries. However, rapid development of clogging in the soil biofilters limits its applicability as an effective technology. This paper aims to understand the occurrence of clogging due to biofilms formation in and over the bedding of soil media. To address this, the organic loading rates (OLRs) were varied in the range of 2.25–11.25 kgCOD/m³·day to create different degree of clogging. Earthworms were inoculated into the soil bedding at the earthworm densities (EWDs) of 0, 5000 and 10,000 earthworms/m³ to study the effect of earthworms introduction on clogging. The degree of clogging was measured using clogging coefficient (CC), hydraulic conductivity and head loss. The study highlights the impact of earthworms on the removal performance and clogging of soil biofilter. For all earthworm densities, head loss and clogging coefficient increased and hydraulic conductivity decreased linearly with organic loading rate. Introduction of earthworms versus no earthworms resulted in lower head loss and clogging coefficient and higher hydraulic conductivity for all organic loading rates, while increasing EWD from 5000 to 10,000 had only marginal effects on all parameters. The study reveals that high organic loading rate activates higher number of microbial sites, in turn causing higher degree of clogging. However, the introduction of earthworms reduces the clogging rate significantly along with enhanced treatment performance. The outcome of this study indicates that incorporation of earthworms into the soil biofilter can reduce the degree of bio-clogging and might provide a highly sustainable, low cost and efficient treatment system for the developing countries.