OBJECTIVES: We evaluated the effect of a nutrition education intervention on bone stress injury (BSI) incidence among female distance runners at two NCAA Division I institutions. METHODS: Historical BSI rates were measured retrospectively (2010-2013); runners were then followed prospectively in pilot (2013-2016) and intervention (2016-2020) phases. The primary aim was to compare BSI rates in the historical and intervention phases. Pilot phase data are included only for descriptive purposes. The intervention comprised team nutrition presentations focused on optimising energy availability plus individualised nutrition sessions for runners with elevated Female Athlete Triad risk. Annual BSI rates were calculated using a generalised estimating equation Poisson regression model adjusted for age and institution. Post hoc analyses were stratified by institution and BSI type (trabecular-rich or cortical-rich). RESULTS: The historical phase included 56 runners and 90.2 person-years; the intervention phase included 78 runners and 137.3 person-years. Overall BSI rates were not reduced from the historical (0.52 events per person-year) to the intervention (0.43 events per person-year) phase. Post hoc analyses demonstrated trabecular-rich BSI rates dropped significantly from 0.18 to 0.10 events per person-year from the historical to intervention phase (p=0.047). There was a significant interaction between phase and institution (p=0.009). At Institution 1, the overall BSI rate dropped from 0.63 to 0.27 events per person-year from the historical to intervention phase (p=0.041), whereas no decline was observed at Institution 2. CONCLUSION: Our findings suggest that a nutrition intervention emphasising energy availability may preferentially impact trabecular-rich BSI and depend on team environment, culture and resources.