In this publication, novel bio-based composites made of epoxidized natural rubber with 50 mol% of epoxidation (ENR-50) are presented. The obtained materials, partially cured with a totally environmentally friendly crosslinking system consisting of natural ingredients, including quercetin and silica, exhibit a self-healing ability resulting from the self-adhesion of ENR-50 and reversible physical forces between the curing agent and the matrix. The impact of natural components on the crosslinking effect in uncured ENR-50 matrix was analyzed based on rheometric measurements, mechanical tests and crosslinking density. The partially crosslinked samples were next cut into two separate pieces, which were instantly contacted together under a small manual press, left at room temperature for a few days for the healing process to occur and finally retested. The healing efficiency was estimated by measuring mechanical properties before and after the healing process and was also confirmed by photos taken using optical and scanning electron microscope (SEM). According to the results, a combination of silica and quercetin is a totally safe, natural and effective crosslinking system dedicated to epoxidized natural rubber. The novel composites containing ingredients safe for human beings exhibit promising self-healing properties with a healing efficiency of up to 45% without any external stimuli and stand a chance of becoming innovative biomedical materials.