The use of nanostructured targets can enhance the energy and quality of accelerated electron and ion beams compared to conventional flat foil targets. Ion acceleration from plastic foil targets having sub-micron thickness embedded with rods of nanometre length using ultra-short intense laser pulses of intensity W cm−2 is investigated using particle-in-cell simulations. The laser and target parameters are tuned to achieve better performance with nanostructured targets compared to flat foils. Several novel features of the ion acceleration process are revealed in this study. A hybrid radiation pressure acceleration-target normal sheath acceleration mechanism using a linearly polarised (LP) laser is found to play a key role in accelerating protons upto ∼300 MeV of energy. The effects of multiple ion species on the acceleration of protons has been studied, and a narrow peak in the proton energy spectrum around ∼100 MeV is observed, which is attributed to the presence of heavier ions in the target.