We implement an extension of the pseudofermion functional renormalization group (PFFRG) method for quantum spin systems that takes into account two-loop diagrammatic contributions. An efficient numerical treatment of the additional terms is achieved within a nested graph construction which recombines different one-loop interaction channels. In order to be fully self consistent with respect to self-energy corrections we also include certain three-loop terms of Katanin type. We first apply this

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... rmalism to the antiferromagnetic J_1-J_2 Heisenberg model on the square lattice and benchmark our results against the previous one-loop plus Katanin approach. Even though the RG equations undergo significant modifications when including the two-loop terms, the magnetic phase diagram -- comprising Néel ordered and collinear ordered phases separated by a magnetically disordered regime -- remains remarkably unchanged. Only the boundary position between the disordered and the collinear phases is found to be moderately affected by two-loop terms. On the other hand, critical RG scales, which we associate with critical temperatures T_c, are reduced by a factor of ∼2 indicating that the two-loop diagrams play a significant role in enforcing the Mermin-Wagner theorem. Improved estimates for critical temperatures are also obtained for the Heisenberg ferromagnet on the 3D simple cubic lattice where errors in T_c are reduced by ∼34%.