We have studied the impact of fluorination on structural, electronic and magnetic properties of phthalocyanine molecules by employing density functional theory (DFT) within generalized gradient approximation (GGA) and hybrid functionals (PBE0, HSE06). The GGA based calculations reveal that fluorinated transition metal phthalocyanine (FMPc) molecules retain planar D-4h symmetry. Mn in FMnPc molecule is found to be in intermediate spin state (3 mu(B)). As the occupation of 3d orbital (n) increases from 5 (FMnPc) up to 8 (FNiPc), magnetic moment reduces smoothly from 3 to 0 mu(B), owing to consequent increase in minority spin population. Hybrid functionals (PBE0, HSE06) largely retain the magnetic state as obtained from GGA. However, PBE0/HSE06 bring about noticeable changes in electronic structure, namely increase in HOMO-LUMO energy gaps as well as reduction of 3d state contribution in frontier orbitals. These results are in good agreement with available experimental data. We further highlight the impact of fluorination on electronic structure: spin state of phthalocyanine molecules remains largely unaffected by fluorination. However, unlike the case of H, states arising from F contribute to density of states near Fermi level, which can be exploited for practical applications such as transport or gas sensing.