There have been two prominent ways of thinking about the relationship between phenomenology and naturalism: the first and more traditional way, in continuity with Husserl’s critique of psychologism, exhibits the incompatibility of phenomenology with all forms of naturalism and positivism; the second and more recent interpretive strategy attempts to naturalize phenomenology and make it consistent with current scientific accounts of consciousness and intentionality. In this paper I argue that despite the fact that Heidegger followed the first path and remained critical of naturalism and positivism throughout his career, there are important moments in the late twenties where his project of a phenomenological ontology is challenged by problems pertaining to naturalism. I show how the question of determining the essence of life and animality as well as the overturning of ontology into metontology offer significant methodological hurdles for Heidegger’s fundamental ontology.