© The Author(s) 2020. Ground stone technology for processing starchy plant foods has its origins in the late Pleistocene, with subsequent intensification and transformation of this technology coinciding with the global emergence of agriculture in the early Holocene. On the island of New Guinea, agriculture first emerges in the highland Wahgi Valley, potentially from c. 9 kya, and clearly evident by 6.5 kya. Approximately 400 km further east in the highland Ivane Valley, long-term occupation sequences span the Holocene and late Pleistocene, but there is currently no direct evidence for wetland agriculture. Here, we report rare evidence for ground stone implements from a secure mid-Holocene archaeological context in the Ivane Valley. The Joe’s Garden site has flaked and ground stone artefacts with significant starch assemblages dating to approximately 4.4 kya. We present the first empirical evidence for the function of stone bowls from a New Guinea highland setting. Usewear and residues indicate the grinding and pounding of endemic starch-rich plant foods. Geometric morphometric analysis of starch grains shows that at least two taxa were processed: Castanopsis acuminatissima (nut) and Pueraria lobata (tuber). This regional example adds to our understanding of the trajectories of diverse plant food exploitation and ground stone technology development witnessed globally in the Holocene.