There has been an enduring interest in primate tool-use and manipulative abilities, most often with the goal of providing insight into the evolution of human manual dexterity, right-hand preference, and what behaviours make humans unique. Chimpanzees (Pan troglodytes) are arguably the most well-studied tool-users amongst non-human primates, and are particularly well-known for their complex nut-cracking behaviour, which has been documented in several West African populations. However, their sister-taxon, the bonobos (Pan paniscus), rarely engage in even simple tool-use and are not known to nut-crack in the wild. Only a few studies have reported tool-use in captive bonobos, including their ability to crack nuts, but details of this complex tool-use behaviour have not been documented before. Here, we fill this gap with the first comprehensive analysis of bonobo nut-cracking in a natural environment at the Lola ya Bonobo sanctuary, Democratic Republic of the Congo. Eighteen bonobos were studied as they cracked oil palm nuts using stone hammers. Individual bonobos showed exclusive laterality for using the hammerstone and there was a significant group-level right-hand bias. The study revealed 15 hand grips for holding differently sized and weighted hammerstones, 10 of which had not been previously described in the literature. Our findings also demonstrated that bonobos select the most effective hammerstones when nut-cracking. Bonobos are efficient nut-crackers and not that different from the renowned nut-cracking chimpanzees of Bossou, Guinea, which also crack oil palm nuts using stones.