Gaseous time projection chambers (TPCs) with high readout segmentation are capable of reconstructing detailed 3D ionization distributions of nuclear recoils resulting from elastic neutron scattering. Using a system of six compact TPCs with pixel ASIC readout, filled with a 70:30 mixture of He:CO2 gas, we analyze the first directional measurements of beam-induced neutron backgrounds in the tunnel regions surrounding the Belle II detector at the SuperKEKB e+e− collider. With the use of 3D recoil tracking, we show that these TPCs are capable of maintaining nearly 100% nuclear recoil purity to reconstructed ionization energies (Ereco) as low as 5keV˙ee. Using a large sample of Monte-Carlo (MC)-simulated 4He, 12C, and 16O recoil tracks, we find consistency between predicted and measured recoil energy spectra in five of the six TPCs, providing useful validation of the neutron production mechanisms modeled in simulation. Restricting this sample to 4He recoil tracks with Ereco>40keV˙ee, we further demonstrate axial angular resolutions within 8° and we introduce a procedure that under suitable conditions, correctly assigns the vector direction to 91% of these simulated 4He recoils. Applying this procedure to assign vector directions to measured 4He recoil tracks, we observe consistency between the angular distributions of observed and simulated recoils, providing first experimental evidence of localized neutron “hotspots” in the accelerator tunnel. Observed rates of nuclear recoils in these TPCs suggest that simulation overestimates the neutron flux from these hotspots. Despite this, we estimate these hotspots to produce the majority of neutron backgrounds in the accelerator tunnel at SuperKEKB’s target luminosity of 6.3×1035cm−2s−1, making them important regions to continue to monitor.