This paper explores the hitherto neglected tradition of natural philosophy (al-ʿilm al-ṭabīʿī) in the Ottoman Empire in the period ca. 1500-1800. While research on the history of Ottoman science and philosophy has made significant progress in recent decades, the discipline of natural philosophy remains severely underresearched. Given the lack of secondary scholarship and edited primary sources on the subject, this study aims to lay a preliminary framework for further research into the Ottoman tradition of natural philosophy. Examining numerous unpublished works on natural philosophy that survive in Turkish manuscript libraries, it offers general answers to questions such as the following: What were the main texts, issues, and debates of natural philosophy in the Ottoman Empire? Who were the principal authors? How did Ottoman scholars understand the discipline of natural philosophy? What was its relationship to other fields of knowledge? What was the institutional framework in which the study of natural philosophy took place? In addressing these questions, this paper argues that Ottoman scholars vigorously pursued natural philosophy throughout the empire's history by presenting three findings. First, the paper shows that the section on natural philosophy in Athīr al-Dīn al-Abharī's (d. 1265) Hidāyat al-ḥikma, Qāḍī Mīr al-Maybudī's (d.1504) commentary on this work, and Muṣliḥ al-Dīn al-Lārī's (d.1571) gloss on al-Maybudī's commentary were tremendously popular in Ottoman scholarly circles. Second, the paper shows that Ottoman scholars wrote numerous glosses and super glosses on al-Maybudī's commentary and al-Lārī's gloss, where they investigated central topics of Aristotelian physics such as atomism, hylomorphism, space, void, motion, and time. Third, the paper shows that the madrasa served as an essential setting for studying natural philosophy and that the discipline was an important part of Ottoman madrasa curricula. Together, these findings radically challenge received views of the natural sciences in the Ottoman Empire, which tend to regard Ottoman scholarly engagements with nature as marginal or characteristically devoid of philosophical orientation.