Conifers often co-occur with angiosperm trees at high altitudes and on infertile soils in tropical rainforests. To explore the mechanism of conifer–angiosperm coexistence, we investigated size structure, growth rate and regeneration of conifers along soil gradient across altitudes and geological substrates. Tree measurements were conducted in ten plots (0.06–1 ha) with varied geology at four altitudes (700, 1700, 2700 and 3100 m) on Mount Kinabalu, Borneo. Conifer juveniles were counted and understory light conditions were analyzed with hemispherical photographs. Size structure of conifers showed inverse-J shape distributions on ultrabasic rocks at ≥1700 m but unimodal or sporadic distributions in other plots. Densities of conifer seedlings and saplings were generally greater on ultrabasic rocks than on non-ultrabasic substrates at comparable altitudes, which concurred with the pattern in understory light conditions. Growth rates over 4 (or 5) years of conifers at 4.8–25 cm diameter were higher than angiosperm trees only under well-lit conditions on non-ultrabasic substrates, but were always similar or higher on ultrabasic rocks even in shaded conditions. Conifers showed continuous regeneration on ultrabasic rocks at ≥1700 m. This suggested that, on infertile soils, competition with angiosperm trees was relaxed and well-lit understory facilitated recruitment of conifers.