The phase formation in the boron-rich section of the Al-Y-B system has been explored by a correlative theoretical and experimental research approach. The structure of coatings deposited via high power pulsed magnetron sputtering from a compound target was studied using elastic recoil detection analysis, electron energy loss spectroscopy spectrum imaging, as well as X-ray and electron diffraction data. The formation of AlYB14 together with the (Y,Al)B6 impurity phase, containing 1.8 at. % less B than AlYB14, was observed at a growth temperature of 800 °C and hence 600 °C below the bulk synthesis temperature. Based on quantum mechanical calculations, we infer that minute compositional variations within the film may be responsible for the formation of both icosahedrally bonded AlYB14 and cubic (Y,Al)B6 phases. These findings are relevant for synthesis attempts of all boron rich icosahedrally bonded compounds with the space group: Imma that form ternary phases at similar compositions.