We present nuclear structure factors that describe the generalized spin-independent coupling of weakly interacting massive particles (WIMPs) to nuclei. Our results are based on state-of-the-art nuclear structure calculations using the large-scale nuclear shell model. Starting from quark- and gluon-level operators, we consider all possible coherently enhanced couplings of spin-1/2 and spin-0 WIMPs to one and two nucleons up to third order in chiral effective field theory. This includes a comprehensive discussion of the structure factors corresponding to the leading two-nucleon currents covering, for the first time, the contribution of spin-2 operators. We provide results for the most relevant nuclear targets considered in present and planned dark matter direct detection experiments: fluorine, silicon, argon, and germanium, complementing our previous work on xenon. All results are also publicly available in a Python notebook.