A series of seven-coordinate pentagonal-bipyramidal (PBP) Cr(III) complexes with pentadentate pyridine-based ligands, 2,6-diacetylpyridine bis(4-methoxybenzoylhydrazone), H2DAPMBH (H2LOCH3) or 2,6-diacetylpyridine bis(benzoylhydrazone), H2DAPBH (H2L) and different axial ligands have been prepared. The reaction of the H2LOCH3 with CrCl2·4H2O in methanol or CrCl3·6H2O in CH3CN led to a novel seven-coordinate pentagonal-bipyramidal (PBP) complex [Cr(HLOCH3)Cl2] (1) with the mono-deprotonated chelating ligand in the equatorial plane and two apical Cl atoms. Then, taking advantage of lability of the apical Cl ligands in 1, a number of PBP CrIII complexes with charged (viz. CH3O−, N3−, CN−, NCS−) and neutral (viz. CH3OH, H2O) apical ligands was obtained and characterized: [Cr(HLOCH3)Cl2]·4CHCl3 (1), [Cr(HLOCH3)Cl2]·CH3OH (1a), [Cr(HLOCH3)(H2O)Cl]PF6·CH3OH (2), [Cr(HL)(H2O)Cl]ClO4·0.25H2O (3), [Cr(HLOCH3)(H2O)2](NO3)2·H2O·C2H5OH (4), [Cr(LOCH3)(CH3OH)(OCH3)]·CH3OH (5), [Cr(HLOCH3)(NCS)2]·1.5H2O (6), [Cr(HLOCH3)(N3)2]·xH2O (7, x = 0.2, 8, x = 0, 9, x = 0, three phases in the same synthesis), [Cr(LOCH3)(N3)2][Na(CH3OH)2]·2CH3OH (10), [Cr(LOCH3)(CN)2][Na(H2O)(C2H5OH)] (11). Single crystal X-ray analysis reveals that all the complexes 1–11 have the PBP geometry with a pentadentate ligand in a form of [HLOCH3]− or [LOCH3]2− in the equatorial plane. The PBP complexes are prone to aggregate into dimers or polymers, either due to strong hydrogen bonds or due to the transformation of terminal ligands into bridging between different metallic centers. All complexes 1–11 exhibit considerable in-plane distortion of the CrN3O2 pentagon due to the shift of the CrIII ion from the central position, which is caused by the strong first-order Jahn-Teller (JT) effect for the high-spin 3d3 configuration in the PBP ligand field. The mechanism of JT distortions is rationalized in terms of DFT calculations. DC magnetic measurements indicate a high-spin (S = 3/2) ground state of complex [Cr(HLOCH3)Cl2]·4CHCl3 (1); theoretical analysis of its magnetic properties reveals negative zero-field splitting energy with the anisotropy parameter D = –1.8 cm−1 and weak dimer-like antiferromagnetic spin coupling J = –0.23 cm−1 between neighboring PBP units [CrIII(HLOCH3)Cl2] mediated by π-stacking of planar H2LOCH3 ligands.