Forests store a large amount of terrestrial carbon, but this storage capacity is vulnerable to wildfire. Combustion, and subsequent tree mortality and soil erosion, can lead to increased carbon release and decreased carbon uptake. Previous work has shown that non-constant fire return intervals over the past 4000 years strongly shaped subalpine forest carbon trajectories. The extent to which fire-regime variability has impacted carbon trajectories in other subalpine forest types is unknown. Here, we explored the interactions between fire and carbon dynamics of 14 subalpine watersheds in Colorado, USA. We tested the impact of varying fire frequency over a ~2000 year period on ecosystem productivity and carbon storage using an improved biogeochemical model. High fire frequency simulations had overall lower carbon stocks across all sites compared to scenarios with lower fire frequencies, highlighting the importance of fire-frequency in determining ecosystem carbon storage. Additionally, variability in fire-free periods strongly influenced carbon trajectories across all the sites. Biogeochemical trajectories (e.g., increasing or decreasing total ecosystem carbon and carbon-to-nitrogen (C:N) ratios) did not vary among forest types but there were trends that they may vary by elevation. Lower-elevations sites had lower overall soil C:N ratios, potentially because of higher fire frequencies reducing carbon inputs more than nitrogen losses over time. Additional measurements of ecosystem response to fire-regime variability will be essential for improving estimates of carbon dynamics from Earth system models.