A series of high quality Zn1−xCoxO thin films were obtained by UHV-magnetron reactive sputtering. Detailed X-ray diffraction, X-ray absorption near edge spectra, and X-ray linear dichroism measurements were used for analyzing the long- and short-range crystalline structure, respectively. These techniques reveal excellent crystalline ordering on both scales for films with oxygen-rich conditions and indicate that Co2+ ions are located on substitutional Zn sites without detectable phase separation. Interestingly, decreasing the structural quality of such Zn1−xCoxO films leads to altered magnetic properties as measured by SQUID magnetometry, ranging from paramagnetism to the emergence of magnetic clustering exhibited by superparamagnetism. In some cases, a small shift of the hysteresis loop is visible after field cooling indicating weak exchange bias typical for the AFM/FM (CoO/Co) system. In the light of detailed structural investigations, the transition regime from paramagnetic to superparamagnetic behavior is discussed.