We present systematic results, based on density functional calculations, for the structure and energetics of $^3$He and $^4$He nanodroplets doped with alkaline earth atoms. We predict that alkaline earth atoms from Mg to Ba go to the center of $^3$He drops, whereas Ca, Sr, and Ba reside in a deep dimple at the surface of $^4$He drops, and Mg is at their center. For Ca and Sr, the structure of the dimples is shown to be very sensitive to the He-alkaline earth pair potentials used in the calculations. The $5s5p←5s^2$ transition of strontium atoms attached to helium nanodroplets of either isotope has been probed in absorption experiments. The spectra show that strontium is solvated inside $^3$He nanodroplets, supporting the calculations. In the light of our findings, we emphasize the relevance of the heavier alkaline earth atoms for analyzing mixed $^3$He-$^4$He nanodroplets, and in particular, we suggest their use to experimentally probe the $^3$He-$^4$He interface.