We present a comprehensive study of the adsorption of bis(phthalocyaninato)lutetium(III) (LuPc$_2$) on highly oriented pyrolytic graphite(0001) (HOPG). The growth and self-assembly of the molecular layers as well as the electronic structure has been investigated systematically using scanning tunnelling microscopy and scanning tunnelling spectroscopy combined with density functional theory (DFT) calculations and molecular mechanics simulations. We reveal that the adsorption of LuPc$_2$ leads to the formation of a square-like close-packed structure on the almost inert surface of HOPG, which is corroborated by simulations. Moreover, we observed a parallel orientation of the LuPc$_2$ molecules in the first monolayer, whereas in subsequent layers an increasing tilt out of the surface plane was found. Tip-sample distance-dependent tunnelling spectroscopy measurements allowed us to detect a shift in the energy positions of the peaks assigned to the lowest unoccupied molecular orbital toward the Fermi energy with decreasing tip-sample separation.
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