This study is aimed to investigate the effect of cobalt, as dopant, on the surface morphologies of nanostructured ZnO thin films. Four different cobalt‐doped ZnO morphologies were prepared by low‐temperature hydrothermal solution deposition, on 2 different substrates—clean glass (CG) and direct‐current magnetron‐sputtered (MS) ZnO glass. An inverse relationship between dopant concentration and grain size was obtained in morphologies obtained from the mixture of solution Zn(NO3)2 + HMT + Co(NO)3.6H2O. No specific relationship exists for those obtained from the mixture of solution Zn(NO3)2 + HMT + PEI + Co(NO)3.6H2O. In general, morphologies obtained from a mixture Zn(NO3)2 + HMT + Co(NO)3.6H2O and Zn(NO3)2 + HMT + PEI + Co(NO)3.6H2O, on MS and CG substrate, vary in grain size (both in length and diameter), crystal population, morphology, film thickness, and crystallinity on films grown on both MS and CG substrates. An increased volumetric size is observed with the increased concentration of cobalt. Lowering the pH—even by 1 magnitude—makes the MS template less effective at aligning the growth of ZnO crystals, giving a decreased crystal packing density.