The toric ideal of a d-dimensional flow polytope has an initial ideal generated by square-free monomials of degree at most d. The toric ideal of a flow polytope of dimension at most four has an initial ideal generated by square-free monomials of degree at most two, with the only exception of the four-dimensional Birkhoff polytope, whose toric ideal has an initial ideal generated by a square-free cubic monomial. The proof is based on a method to classify certain compressed flow polytopes, and a construction of a quadratic pulling triangulation of them. Along the way compressed flow polytopes are classified up to dimension four, and their Ehrhart polynomials are computed.