Naturalists leveraging Cognitive Science of Religion (CSR) mechanisms—such as Hyperactive Agency Detection, theory of mind, and teleological biases—have formulated debunking arguments against supernatural beliefs across five axes: content incompatibility, unreliability, naturalization of experience, consensus critique, and religious diversity. This article evaluates the logical and empirical success of these arguments in undermining religious rationality. It argues that they fail due to three fundamental deficiencies: committing the genetic fallacy by conflating discovery with justification; relying on question-begging naturalistic presuppositions; and neglecting the ethical-metaphysical content of beliefs alongside cultural corrective factors. The study’s innovation lies in systematically applying Inference to the Best Explanation (IBE) as an objective adjudicative framework. By employing criteria like explanatory scope, coherence, parsimony, and predictive power, this method avoids epistemic relativism. Combining “truth-tracking” and “divine design” strategies, the article demonstrates that theism offers a superior explanation to naturalism across all five domains. Consequently, the CSR debate is revealed not merely as scientific confrontation, but as a contest between metaphysical worldviews. Until presuppositions are assessed, debunking arguments remain circular. Their ineffectiveness stems from neglecting that humans, as meaning-seeking creatures, shape beliefs within lived experiences and moral intuitions. Ultimately, theism is established not as emotional response, but as a rational hypothesis explaining the totality of religious phenomena more comprehensively than naturalistic alternatives, reaffirming its epistemic viability against cognitive reductionism.