Searches for invisible Higgs decays at the Large Hadron Collider constrain dark matter Higgs-portal models, where dark matter interacts with the Standard Model fields via the Higgs boson. While these searches complement dark matter direct-detection experiments, a comparison of the two limits depends on the coupling of the Higgs boson to the nucleons forming the direct-detection nuclear target, typically parameterized in a single quantity $f_N$. We evaluate $f_N$ using recent phenomenological and lattice-QCD calculations, and include for the first time the coupling of the Higgs boson to two nucleons via pion-exchange currents. We observe a partial cancellation for Higgs-portal models that makes the two-nucleon contribution anomalously small. Our results, summarized as $f_N=0.308(18)$, show that the uncertainty of the Higgs-nucleon coupling has been vastly overestimated in the past. The improved limits highlight that state-of-the-art nuclear physics input is key to fully exploiting experimental searches.