While long-term organic fertilizer (OF) applications tend to decrease copper (Cu) and zinc (Zn) availability in agricultural soils, earthworm bioturbation has been reported to have the opposite effect. Thus, the consequences of OF amendments in earthworm-inhabited soils on Cu and Zn bioavailability to earthworms are still under debate. Here, we assessed the effect of a decade of agronomically realistic OF applications on Cu and Zn availability in earthworm-inhabited soils and the consequences on Cu and Zn bioavailability to earthworms. An epi-endogeic species (Dichogaster saliens) was exposed in microcosms to three field-collected soils that had received either no, mineral, or organic fertilization for a decade. Dissolved organic matter (DOM) properties (i.e., concentration, aromaticity, and binding properties toward Cu), pH, and Cu and Zn availability (i.e., total concentration and free ionic activity) were determined in the solution of the soil containing earthworms. Cu and Zn bioavailability was assessed by measuring the net accumulation (ng) and concentration of Cu and Zn in earthworms (mg kg−1). Despite soil Cu and Zn contamination induced by a decade of OF applications, organic fertilization induced an increase in soil pH and DOM properties that drove the reduction of Cu and Zn availability in earthworm-inhabited soils, while bioturbation had little effect on soil pH, DOM properties, and Cu and Zn availability. Consistently, Cu and Zn bioavailability to earthworms did not increase with OF applications. From an ecotoxicological perspective, our results suggest that agronomically realistic applications of OF for a decade should not pose a risk to earthworms in terms of Cu and Zn net accumulation, but further studies have to be undertaken to understand consequent long-term toxicity after exposure.