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Tropical montane forests (TMFs) play an important role as a carbon reservoir at a global scale. However, there is a lack of a comprehensive understanding on the variation in carbon storage across TMF compartments [namely aboveground biomass (AGB), belowground biomass (BGB), and soil organic matter] along altitudinal and environmental gradients and their potential trade-offs. This study aims to: 1) understand how carbon stocks vary along altitudinal gradients in Andean TMFs, and; 2) determine the influence of climate, particularly precipitation seasonality, on the distribution of carbon stocks across different forest compartments. The study was conducted in sixty 0.1 ha plots along two altitudinal gradients at the Podocarpus National Park (Ecuador) and Río Abiseo National Park (Peru). At each plot, we calculated the amount of carbon in AGB (i.e. aboveground carbon stock, AGC), BGB (i.e. belowground carbon stock, BGC), and soil organic matter (i.e. soil organic carbon stock, SOC). The mean total carbon stock was 244.76 ± 80.38 Mg ha–1 and 211.51 ± 46.95 Mg ha–1 in the Ecuadorian and Peruvian plots, respectively. Although AGC, BGC, and SOC showed different partitioning patterns along the altitudinal gradient both in Ecuador and Peru, total carbon stock did not change with altitude in either site. The combination of annual mean temperature and precipitation seasonality explained differences in the observed patterns of carbon stocks across forest compartments between the two sites. This study suggests that the greater precipitation seasonality of colder, higher altitudes may promote faster turnover rates of organic matter and nutrients and, consequently, less accumulation of SOC but greater AGC and BGC, compared to those sites with lesser precipitation seasonality. Our results demonstrate the capacity of TMFs to store substantial amounts of carbon and suggest the existence of a trade-off in carbon stocks among forest compartments, which could be partly driven by differences in precipitation seasonality, especially under the colder temperatures of high altitudes.