Phytoremediation is a cost-effective and ecologically friendly process that involves the use of plants to uptake, accumulate, translocate, stabilize, or degrade pollutants. The present study was conducted to demonstrate the potential of pea (Pisum sativum L. spp. sativum) cultivar Blauwschokker to phytostimulate biodiesel degradation in an agricultural soil, considering the influence of biological remediation on selected physiological parameters of plants and the amount and activity of soil microflora. Biodiesel was spiked into soil in dose of 50 g kg−1 of dry mass soil. The results of the study showed that the rate of biodiesel degradation in the vegetated soil was higher than that occurring by natural attenuation. At the same time, biodiesel showed a positive effect on the growth, development, and activity of soil bacteria and fungi. Moreover, the obtained results showed an improvement in physiological parameters of plants, including an increase in chlorophyll a and total chlorophyll content and higher relative water content in leaves in the presence of biodiesel.