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We consider the recently proposed possibility that dark energy (DE) and baryons may scatter through a pure momentum exchange process, leaving the background evolution unaffected. Earlier work has shown that, even for barn-scale cross-sections, the imprints of this scattering process on linear cosmological observables is too tiny to be observed. We therefore turn our attention to non-linear scales, and for the first time investigate the signatures of DE-baryon scattering on the non-linear formation of cosmic structures, by running a suite of large N-body simulations. The observables we extract include the non-linear matter power spectrum, halo mass function, and density and baryon fraction profiles of halos. We find that in the non-linear regime the signatures of DE-baryon scattering are significantly larger than their linear counterparts, due to the important role of angular momentum in collapsing structures, and potentially observable. The most promising observables in this sense are the baryon density and baryon fraction profiles of halos, which can potentially be constrained by a combination of kinetic Sunyaev-Zeldovich (SZ), thermal SZ, and weak lensing measurements. Overall, our results indicate that future prospects for cosmological and astrophysical direct detection of non-gravitational signatures of dark energy are extremely bright.