Fire regimes across the globe have been altered through changes in land-use, land management and climate conditions. Understanding how these modified fire regimes impact vegetation structure and dynamics is essential for informed biodiversity conservation and carbon management in savanna ecosystems. We used a long-term fire experiment at the Territory Wildlife Park (TWP), northern Australia, to investigate the consequences of altered fire regimes for habitat structure and aboveground carbon storage. We mapped vegetation three-dimensional (3D) structure in high spatial resolution with airborne LiDAR, across 18 replicated 1ha plots of varying fire frequency and season treatments. We used LiDAR-derived canopy height and cover metrics to extrapolate field-based measures of woody biomass to the full extent of the experimental site (R2=0.82, RMSE=7.35tCha−1), and analysed differences in aboveground carbon storage and 3D structure among treatments. Woody canopy cover and biomass were highest in the absence of fire (76% and 39.8tCha−1) and lowest in plots burnt late in the dry season on a biennial basis (42% and 18.2tCha−1). Woody canopy vertical profiles differed among all six fire treatments, with greatest divergence in height classes 5m. Our results highlight the large extent to which fire management can shape 3D structural patterns in savanna landscapes, even over time frames as short as a decade. The structural profile changes shown here, and the quantification of carbon reduction under late dry season burning, have important implications for faunal habitat conservation and carbon sequestration/emission reduction initiatives in the region.