Natural hazards are one of the destructive phenomena that pose a significant hazard to humans, property, and the economy, among others. One of the most recurring natural hazards is flooding, which is caused by typhoons, monsoons, and heavy rainfall and has been one of the main concerns of the Philippines in recent years. The study’s results will provide information on the factors affecting flood disaster preparedness by integrating the Theory of Planned Behavior (TPB) and the Protection Motivation Theory (PMT). A total of 509 individuals answered an online survey questionnaire with 52 adapted questions. Structural equation modeling (SEM) revealed that risk perception (RP), media (M), and personal experience (PE) had an effect on perceived severity (PS) and perceived vulnerability (PV), which consequently affected the attitude toward the behavior (ATB), social norms (SN), and perceived behavioral control (PBC). It was determined that ATB, SN, and PBC significantly affected adapted behavior (AB), which consequently led to intention to follow (ITF) and perceived prevention (PP). After analyzing the data, it was revealed that 56.2% of female respondents were said to be more disaster resilient compared to males. This is the first study to determine the perceived prevention of disaster preparedness and mitigation in flood-prone areas in the Philippines. The results will be beneficial to academicians and government officials in developing determining factors that affect flood disaster preparedness. Lastly, a deeper understanding of how AB is the most significant variable may be further researched to improve the paper.