Improvements in the spatial resolution of synchrotron-based X-ray probes have reached the nano-scale and they, nowadays, constitute a powerful platform for the study of semiconductor nanostructures and nanodevices that provides high sensitivity without destroying the material. Three complementary hard X-ray synchrotron techniques at the nanoscale have been applied to the study of individual nanowires (NWs) containing non-polar GaN/InGaN multi-quantum-wells. The trace elemental sensitivity of X-ray fluorescence allows one to determine the In concentration of the quantum wells and their inhomogeneities along the NW. It is also possible to rule out any contamination from the gold nanoparticle catalyst employed during the NW growth. X-ray diffraction and X-ray absorption near edge-structure probe long- and short-range order, respectively, and lead us to the conclusion that while the GaN core and barriers are fully relaxed, there is an induced strain in InGaN layers corresponding to a perfect lattice matching with the GaN core. The photoluminescence spectrum of non-polar InGaN quntum wells is affected by strain and the inhomogeneous alloy distribution but still exhibits a reasonable 20% relative internal quantum efficiency.