The impact of core fluorination on the phase behaviour of supramolecular hydrogen-bonded liquid crystals (HBLCs) is investigated in detail. Therefore, different types of HBLCs were synthesized using two benzoic acid derivatives as proton donors, namely, 4-octyloxybenzoic acid and octylbenzoic acid. The two acids were combined through intermolecular hydrogen-bonding with alkoxyazopyridine derivatives as proton acceptors. Three different types of azopyridines were used either without fluorine substitution or with one lateral fluorine substituent at different positions. The study proved the importance of using core fluorination as a significant tool to modify the liquid crystalline behaviour of HBLCs, where all azopyridines are non-mesomorphic and almost all their complexes exhibit enantiotropic mesophases. The formation of the hydrogen bond between the complementary components was confirmed using FTIR and 1H NMR spectroscopy, while the liquid crystalline self-assembly of the HBLCs was investigated in detail using polarized light microscope (PLM) and differential scanning calorimetry (DSC). Depending on the type of the terminal chain on the benzoic acid derivative and on the position of the lateral fluorine substituent different types of mesophases including nematic (N), smectic A (SmA) and smectic C (SmC) phases were observed. Finally, under UV light illumination all the prepared HBLCs show cis-trans photoisomerization resulting in tuning the liquid crystalline phases, which is of importance for industrial applications.