Bone stress injuries (BSIs) frequently occur in the leg and foot long bones of female distance runners. A potential means of preventing BSIs is to participate in multidirectional sports when younger to build a more robust skeleton. The current cross-sectional study compared differences in tibia, fibula, and second metatarsal diaphysis size, shape, and strength between female collegiate-level athletes specialized in cross-country running (RUN, n = 16) and soccer (SOC, n = 16). Assessments were performed using high-resolution peripheral quantitative computed tomography and outcomes corrected for measures at the radius diaphysis to control for selection bias and systemic differences between groups. The tibia in SOC had a 7.5 % larger total area than RUN, with a 29.4 % greater minimum second moment of area (IMIN) and 8.2 % greater estimated failure load (all p ≤ 0.02). Tibial values in SOC exceeded reference data indicating positive adaptation. In contrast, values in RUN were similar to reference data suggesting running induced limited tibial adaptation. RUN did have a larger ratio between their maximum second moment of area (IMAX) and IMIN than both SOC and reference values. This suggests the unidirectional loading associated with running altered tibial shape with material distributed more in the anteroposterior (IMAX) direction as opposed to the mediolateral (IMIN) direction. Comparatively, SOC had a similar IMAX/IMIN ratio to reference data suggesting the larger tibia in SOC resulted from multiplane adaptation. In addition to enhanced size and strength of their tibia, SOC had enhanced structure and strength of their fibula and second metatarsal. At both sites, polar moment of inertia was approximately 25 % larger in SOC compared to RUN (all p = 0.03). These data support calls for young female athletes to delay specialization in running and participate in multidirectional sports, like soccer, to build a more robust skeleton that is potentially more protected against BSIs.