Self-assembled, atomic diffusion controlled growth of InN quantum dots was realized on the side facets of dislocation-free and c-oriented GaN nanowires having a hexagonal cross-section. The nanowires were synthesized by selective area metal organic vapor phase epitaxy. A 3 Å thick InN wetting layer was observed after growth, on top of which the InN quantum dots formed, indicating self-assembly in the Stranski-Krastanow growth mode. We found that the InN quantum dots can be tuned to nucleate either preferentially at the edges between GaN nanowire side facets, or directly on the side facets by tuning the adatom migration by controlling the precursor supersaturation and growth temperature. Structural characterization by transmission electron microscopy and reciprocal space mapping show that the InN quantum dots are close to be fully relaxed (residual strain below 1%) and that the c-planes of the InN quantum dots are tilted with respect to the GaN core. The strain relaxes mainly by the formation of misfit dislocations, observed with a periodicity of 3.2 nm at the InN and GaN hetero-interface. The misfit dislocations introduce I1 type stacking faults (…ABABCBC…) in the InN quantum dots. Photoluminescence investigations of the InN quantum dots show that the emissions shift to higher energy with reduced quantum dot size, which we attribute to increased quantum confinement.