According to methodological naturalism, scientists must use only scientific methods in their scientific activities. methodological naturalism means setting aside prior theological and metaphysical beliefs in the practice of science to maintain neutrality. Proponents consider it a fundamental methodological requirement of science. However, the question arises: Does adherence to this doctrine provide science with sufficient capacity to explain all phenomena, and does it pose challenges to science? This documentary-analytical study compares the views of Alvin Plantinga and Michael Ruse. Both philosophers challenge methodological naturalism, but from different perspectives. Ruse argues that methodological naturalism fails to explain fundamental concepts such as existence, ethics, purpose, and consciousness. Therefore, he adopts an agnostic stance and considers the inference of ontological naturalism from methodological naturalism unjustified. In contrast, Plantinga views methodological naturalism as fundamentally flawed, claiming that science is not neutral and thus advocates for Augustinian science. The authors find both perspectives problematic, citing issues such as epistemic halt, methodological limitations, relativism, and lack of comprehensiveness. The naturalistic approach itself faces challenges such as reductionism and neglect of contextual understanding. Therefore, the authors suggest an integrated approach.