The underlying mechanism for deterioration in cardiometabolic health after major natural disasters is unknown. We leveraged natural experiment data stemming from the 2011 Great East Japan Earthquake and Tsunami (n = 1165) to examine whether specific types of post-disaster accommodations explain the association between disaster-related property damage and objectively measured cardiometabolic profiles of older disaster survivors. Causal mediation analysis showed that relocation to trailer-style temporary shelters largely mediated the associations between home loss and unhealthy changes in anthropometric measures (72.6% of 0.65 kg/m for body mass index and 62.3% of 3.89 cm for waist circumference), but it did not mediate the associations with serum lipid measures. This study demonstrates that there are outcome-specific pathways linking disaster damage and health of survivors.