We study the algebraic $K$-theory and Grothendieck-Witt theory of proto-exact categories of vector bundles over monoid schemes. Our main results are the complete description of the algebraic $K$-theory space of an integral monoid scheme $X$ in terms of its Picard group $operatorname{Pic}(X)$ and pointed monoid of regular functions $Gamma(X, mathcal{O}_X)$ and a description of the Grothendieck-Witt space of $X$ in terms of an additional involution on $operatorname{Pic}(X)$. We also prove space-level projective bundle formulae in both settings.