<p>This study presents the first two-arm randomized controlled trial (RCT) conducted in resource-constrained rural areas of Pakistan to evaluate the effectiveness of a theory-based online risk communication intervention grounded in Protection Motivation Theory and the Theory of Planned Behavior (PMT-TPB) in influencing theoretical constructs and preferences for waste management policies. The trial included 335 participants in the experimental group and 336 in the control group, representing two diverse ethnicities with different health statuses. A two-month post-test comparison showed that the intervention had a significant positive effect on all PMT-TPB theoretical concepts, including waste separation intention (WSI) in the experimental group. Similarly, an increased likelihood of endorsing IoT-connected separate waste bins, recycling plants, waste-to-energy facilities, civic education and awareness, economic incentives, public praise, penalties, and waste charges, with a lesser likelihood of supporting the construction of a rural sanitary landfill site was observed. Subgroup analysis indicated that the intervention’s effectiveness was consistent across ethnic and health status subgroups, except for the construction of a rural sanitary landfill, where support decreased only among the respondents of Pashtun ethnicity. These findings provide valuable insights into how effective interventions can reshape perceptions and behavior, thereby bridging the gap between policy development and community acceptance.</p>