We report the structure and emission properties of ternary (In,Ga)N nanowires (NWs) embedded with self-assembled quantum dots (SAQDs). InGaN NWs are fabricated by the reaction of In, Ga and NH3 via a vapor-liquid-solid (VLS) mechanism, using Au as the catalyst. By simply varying the growth temperature, In-rich or Ga-rich ternary NWs have been produced. X-ray diffraction, Raman studies and transmission electron microscopy reveal a phase-separated microstructure wherein the isovalent heteroatoms are self-aggregated, forming SAQDs embedded in NWs. The SAQDs are observed to dominate the emission behavior of both In-rich and Ga-rich NWs. Temperature-dependent photoluminescence (PL) measurements indicate relaxation of excited electrons from the matrix of the Ga-rich NWs to their embedded SAQDs. A multi-level band schema is proposed for the case of In-rich NWs, which showed an anomalous enhancement in the PL peak intensity with increasing temperature accompanies with red shift in its peak position.