We apply the subtracted kernel method (SKM), a renormalization approach based on recursive multiple subtractions performed in the kernel of the scattering equation, to the chiral nucleon–nucleon (NN) interactions up to next-to-next-to-leading-order. We evaluate the phase-shifts in the 1S0 channel at each order in Weinberg’s power counting scheme and in a modified power counting scheme which yields a systematic power-law improvement. We also explicitly demonstrate that the SKM procedure is renormalization group invariant under the change of the subtraction scale through a non-relativistic Callan–Symanzik flow equation for the evolution of the renormalized NN interactions.