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The island of New Guinea occupies the northern margin of the Australian Plate and has experienced rapid northward motion over the past ~30 million years. This movement led to collisions with volcanic island arcs on the Pacific Plate, producing some of Earth’s youngest mountain belts. These tectonic interactions not only reshaped the landscape but also created conditions for species diversification by fragmenting habitats, isolating ecosystems, and expanding land area. As volcanic islands accreted and were progressively uplifted, montane environments became separated from surrounding lowlands, promoting endemism across individual mountain ranges, exemplified by taxa such as Birds of Paradise. Understanding when and how these volcanic islands formed and collided with the Australian margin is therefore critical for linking tectonic processes with palaeo-landscape evolution and the development of megadiverse regions such as New Guinea.The Cyclops Mountains provide a key example of this process. They represent a remnant volcanic island arc and ophiolite complex that was obducted onto the northern Australian margin in the early Miocene. Along with other accreted island fragments across northern New Guinea, the Cyclops Mountains were further uplifted and became increasingly isolated from lowland environments during final arc–continent collision in the Pliocene. This tectonic isolation fostered the development of distinct montane ecosystems that today host highly localised species, including Attenborough’s long-beaked echidna (Zaglossus attenboroughi), highlighting the dominant influence that collisional tectonic processes have had on New Guinea’s biogeographic evolution.Here we present a new workflow for resolving the links between tectonic processes and palaeo-ecosystem change in active collision zones. By integrating geological fieldwork, palaeogeographic reconstructions, geochronology, biostratigraphy, and organic biomarker analyses, we reconstruct the emergence, submergence, and uplift of volcanic islands in the Cyclops Mountains from the Eocene through the Plio-Pleistocene, providing new insight into how tectonics shape long-term environmental and biological change.