Over the past decade, in contrast to the traditional analytic version of metaphysics, a brand of metaphysics that prioritizes collaboration and corroboration with sciences has emerged in the form of scientific metaphysics. While there has been a shift from the methodological dependence of analytic metaphysis on intuition, and conceptual analysis to the methodological preference for empirically-motivated metaphysical insights in scientific metaphysics, such a shift has not penetrated the foundational aims. Scientific metaphysics continues to probe the nature and structure of reality, much like its analytic counterpart and in this process, develops ontologies. Broadly two kinds of ontologies are furnished - global metaphysical ontologies and local scientific ontologies. In this paper, I highlight the challenges with developing such ontologies in scientific metaphysics. With Ladyman-Ross’ Information Theoretic Structural Realism as a case in point, I contest that the former suffers from representational indeterminacy and redundancy. Further, I note the possibility that eventually, local scientific ontologies might be replaced by scientific theories and in such a scenario, the former are best conceived as interim metaphysical supports for the latter.