We study the algebraic $K$-theory and Grothendieck-Witt theory of proto-exact categories, with a particular focus on classes of examples of $mathbb{F}_1$-linear nature. Our main results are analogues of theorems of Quillen and Schlichting, relating the $K$-theory or Grothendieck-Witt theories of proto-exact categories defined using the (hermitian) $Q$-construction and group completion.