A series of chemically prepared Co2+-doped ZnO colloids has been surface modified either by growing shells of ZnSe or by the in situ encapsulation in poly(styrene). The surface modification effects using these two distinct chemical strategies on the magnetic properties of the nanocrystals were probed by electron paramagnetic resonance (EPR). Structural characterization by means of x-ray diffraction and transmission electron microscopy gave no evidence of second phase formation within the detection limits of the used equipment. The EPR analysis was carried out by simulations of the powderlike EPR spectra. The results confirm that in the core of these nanocrystals Co was incorporated as Co2+, occupying the Zn2+ sites in the wurtzite structure of ZnO. Additionally we identify two Co signals stemming from the nanocrystals’ shell. The performed surface modifications clearly change the relative intensity of the EPR spectrum components, revealing the core and shell signals.