In this study, novel eco-friendly blends based on environmental-friendly polymers and compatibilizers, such as poly(ϵ-caprolactone) (PCL), cis-1,4-polyisoprene (PI), soybean lecithin (SOLE) and acrylated-epoxidized soybean oil (AESO), have been prepared in order to suggest a biodegradable joining tool used for plant grafting in agriculture, which will be competitive from the environment and economic points of view against conventional nonbiodegradable tools. PCL/PI blends, in which the portion of PCL was 75 and 50, were mixed with a compatibilizer by a melt-blending technique. The resulting blends were investigated by thermogravimetric analysis, differential scanning calorimetry and scanning electron microscopy and also their mechanical properties were determined. Afterwards, the blend films were buried in the soil. Remarkable level of weight loss was achieved in 6 weeks, ∼46%. The results showed that the addition of SOLE helped to improve the compatibility between PCL and PI due to its amphipathic property, and, besides, accelerated the weight loss of the films in soil, increasing microorganism growth on the film.