The Baldoni–Vergne volume and Ehrhart polynomial formulas for flow polytopes are significant in at least two ways. On one hand, these formulas are in terms of Kostant partition functions, connecting flow polytopes to this classical vector partition function, fundamental in representation theory. On the other hand, the Ehrhart polynomials can be read off from the volume functions of flow polytopes. The latter is remarkable since the leading term of the Ehrhart polynomial of an integer polytope is its volume! Baldoni and Vergne proved these formulas via residues. To reveal the geometry of these formulas, the second author and Morales gave a fully geometric proof for the volume formula and a partial generating function proof for the Ehrhart polynomial formula. The goal of the present paper is to provide a fully geometric proof for the Ehrhart polynomial formula for flow polytopes.