The magnetic configurations of cylindrical Co-rich CoNi nanowires have been quantitatively analyzed at the nanoscale by electron holography and correlated to local structural and chemical properties. The nanowires display grains of both face-centered cubic (fcc) and hexagonal close packed (hcp) crystal structures, with grain boundaries parallel to the nanowire axis direction. Electron holography evidences the existence of a complex exotic magnetic configuration characterized by two distinctly different types of magnetic configurations within a single nanowire: an array of periodical vortices separating small transverse domains in hcp-rich regions with perpendicular easy axis orientation and a mostly axial configuration parallel to the nanowire axis in regions with fcc grains. These vastly different domains are found to be caused by local variations in the chemical composition modifying the crystalline orientation and/or structure, which give rise to change in magnetic anisotropies. Micromagnetic simulations, including the structural properties that have been experimentally determined, allow for a deeper understanding of the complex magnetic states observed by electron holography.