Background Natural disasters and public health crises can disrupt communities' capacities to implement important public health programs. A nationwide implementation of an evidence-based HIV prevention program, Focus on Youth in The Caribbean (FOYC) and Caribbean Informed Parents and Children Together (CImPACT), in The Bahamas was disrupted by Hurricane Dorian and the COVID-19 pandemic, especially in its more remote, Family Islands. We explored the teacher- and school-level factors that affected implementation of the program in these islands during those disruptions. Methods Data were collected from 47 Grade 6 teachers and 984 students in 34 government elementary schools during the 2020-2021 school year. Teachers completed a pre-implementation questionnaire to record their characteristics and perceptions that might affect their implementation fidelity and an annual program training workshop. School coordinators and high-performing teachers acting as mentors received additional training to provide teachers with monitoring, feedback, and additional support. Teachers submitted data on their completion of the 9 sessions and 35 core activities of FOYC + CImPACT. The fidelity outcomes were the number of sessions and core activities taught by teachers. Results On average, teachers taught 60% of sessions and 53% of core activities. Teachers with very good school coordinators (34% of teachers) taught more activities than those with satisfactory (43%) or no (34%) school coordinator (27.5 vs. 16.8 vs. 14.8, F = 12.86, P < 0.001). Teachers who had attended online training or both online and in-person training taught more sessions (6.1 vs. 6.2 vs. 3.6, F = 4.76, P < 0.01) and more core activities (21.1 vs. 20.8 vs. 12.6, F = 3.35, P < 0.05) than those who received no training. Teachers' implementation was associated with improved student outcomes (preventive reproductive health skills, self-efficacy, and intention). Conclusions The Hurricane Dorian and the COVID-19 pandemic greatly disrupted education in The Bahamas Family Islands and affected implementation of FOYC + CImPACT. However, we identified several strategies that supported teachers' implementation following these events. Teacher training and implementation monitoring increased implementation fidelity despite external challenges, and students achieved the desired learning outcomes. These strategies can better support teachers' implementation of school-based interventions during future crises.