While it is true that heavy metals accumulate in soil easily, their removal is difficult. The organic fraction of municipal solid waste can be recycled into compost, although frequent application of biowaste may lead to the accumulation of heavy metals in soil. There is no deep-rooted tradition in Lithuania to make and use various biowaste composts, including the ones produced from municipal waste. The objective of this study has been to compare the accumulation of heavy metals in different parts of oilseed pumpkin fruit depending on the chemical composition of the compost the pumpkin plants had been supplied. The content of heavy metals (HM) was determined in the soil before the plant-growing experiment, and in biowaste composts of different origin. Green waste (GW) and municipal solid waste (MSW) composts were applied to soil as fertiliser. Heavy metal concentrations in the skin, flesh and seeds of the analysed pumpkin fruits did not exceed the maximum permissible concentrations established by the EU norms. Seeds of the investigated pumpkin cultivar Olivia are more sensitive to the effect of heavy metal accumulation than the other morphological fruit parts (skin and flesh). The highest amounts of the investigated heavy metals, except Cr, were determined in the seeds, while the lowest ones, except Cu, in the flesh of oilseed pumpkin fruits. The amount of heavy metals in pumpkin biomass was not directly related to their concentrations in the soil, which proves the fact that the transfer of heavy metals from soil to plant is determined primarily by metal bioavailability and by a plant species.