We define and study the $K$-theory of exact categories with coefficients in endofunctors of spectra in analogy with Mitchell's homology of categories. Generalizing computations of McCarthy, we determine, for a discrete ring $R$, the $K$-theory of the exact category of finitely-generated projective $R$-modules with coefficients in the $n$-fold smash product functor. This computation allows us to analyze the effects of applying this functorial construction to the Goodwillie Taylor tower of a homotopy endofunctor of spectra. In the case of $\Sigma^\infty\Omega^\infty$, the associated tower recovers the Taylor tower of relative $K$-theory as computed by Lindenstrauss and McCarthy.