Part I was concerned with epistemic stances: epistemic attitudes to scientific ontology. In Part II we turn to metaphysical stances as they feature in biology: metaphysical positions construed as stances that can act as presuppositions of and influences on biological science. We shall consider three debates in the metaphysics of biology: that between functionalists and structuralists, that between punctuationists and gradualists, and that between reductionists and holists. I shall argue that in each case, the relevant positions ought to be construed as metaphysical stances rather than factual beliefs.