Axial Seamount is a submarine volcano on the Juan de Fuca Ridge with enhanced magma supply from the Cobb Hotspot. Here we compare several deformation model configurations to explore how the spatial component of Axial’s deformation time series relates to magma reservoir geometry imaged by multi-channel seismic (MCS) surveys. To constrain the models, we use vertical displacements from pressure sensors at seafloor benchmarks and repeat autonomous underwater vehicle (AUV) bathymetric surveys covering 2016-2020. We show that implementing the MCS-derived 3D main magma reservoir (MMR) geometry with uniform pressure in a finite element model poorly fits the geodetic data. To test the hypothesis that there is compartmentalization within the MMR that results in heterogeneous pressure distribution, we compare analytical models using various horizontal sill configurations constrained by the MMR geometry. Using distributed pressure sources significantly improved the Root Mean Square Error (RMSE) between the inflation data and the models by an order of magnitude. The RMSE between the AUV data and the models was not improved as much, likely due to the relatively larger uncertainty of the AUV data. The models estimate the volume change for the 2016-2020 inter-eruptive inflation period to be between 0.054-0.060 km3 and suggest that the MMR is compartmentalized, with most magma accumulating in sill-like bodies embedded in crystal mush along the western-central edge of the MMR. The results reveal the complexity of Axial’s plumbing system and demonstrate the utility of integrating geodetic data and seismic imagery to gain deeper insights into magma storage at active volcanoes.