Low solubility dopant-host systems are well suited to study secondary phase segregation-microstructure dependence. We discuss the effect of microstructure on secondary phase segregation in epitaxial/oriented ZnO thin films with Cr as an unfavorable dopant (Cr:ZnO). Since differences in thin film microstructure are a function of the substrate and its orientation, simultaneous chemical vapor depositions were carried out on single crystals of Si (100), c-axis oriented Al2O3 (c-ALO), and r-axis oriented Al2O3 (r-ALO) resulting in epitaxial film growth on r-ALO and c-axis oriented film growth on Si and c-ALO, with a difference in vertical grain boundary density. To enhance the analysis sensitivity to the microstructure difference, the thickness of Cr:ZnO films was maintained at ∼50 nm. High-resolution transmission electron microscopy (HRTEM) analysis indicates uniform stress distribution in Cr:ZnO grown on r-ALO. Surface sensitive x-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectroscopy (TOF-SIMS) techniques were utilized for analysis of the data. We observe that a higher grain boundary density and the presence of an amorphous layer at the interface for films grown on Si(100) single crystal led to interfacial Cr-based secondary phase segregation as opposed to lower grain boundary density and epitaxial films grown on c-ALO and r-ALO single crystals, respectively. We also discuss the effects of trace carbon solubility on the film microstructure/secondary phase segregation relationship.