Currently there is limited knowledge as to the morphology of bacteriogenic manganese (Mn)-oxide minerals, making it difficult to identify Mn minerals from geologic deposits as being biotic or abiotically formed. When investigating mineral deposits it is critical to understand what environmental processes lead to mineral formation in order to accurately interpret the information locked inside each mineral. This study aims to characterize the morphology, structural variability, and microbe-mineral association of bacteriogenic Mn(III/IV) oxides produced by Mn(II/III)-oxidizing bacteria, using pure cultures of three known Mn-oxidizing bacteria. Morphology and localization of bacteriogenic Mn-oxides was characterized using high resolution scanning electron (HR-SEM) and transmission electron microscopy (TEM). We found that the morphology of bacteriogenic Mn-oxides varies between bacterial species, and that the localization of Mn oxidizing enzymes determines if Mn-oxides are closely associated with the cellular surface or form in exopolysaccharides (EPS). Knowledge acquired from this study illustrates the complexity of identifying bacteriogenic Mn-oxides and oxidation products from more complex natural environmental settings like ancient geologic deposits.