Two penta-coordinate complexes of the general formula [Co(Ln)(NCS)]ClO4, where L1 = {bis[(3,5-dimethyl-1H-pyrazol-1-yl)ethyl]-[(3,4-dimethoxypyridin-2-yl)methyl]}amine and L2 = {bis[(3,5-dimethyl-1H-pyrazol-1-yl)ethyl]-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]}amine, have been synthesized and thoroughly characterized. Each of the cobalt(ii) atoms is penta-coordinated in the {CoN5} donor set with a distorted square-pyramidal geometry in [Co(L1)(NCS)]ClO4·MeOH (1), while the vicinity of the central atom can be described as a distorted trigonal-bipyramidal geometry in [Co(L2)(NCS)]ClO4 (2) as revealed using the SHAPE analysis. Differences in interatomic parameters among the cobalt(ii) and donor atoms in 1 and 2 have definite impact on the magnetic features of both compounds. The complexes show an easy-axis magnetic anisotropy (D = -38.5 cm-1 for 1 and D = -8.5 for 2), and both complexes reveal a large rhombicity with E/D = 0.21 for 1 and E/D = 0.29 for 2. The ZFS parameters (g, D and E) were also calculated using CASSCF/NEVPT2 methods and they are in good agreement with those determined from experimental data. A frequency dependent out-of-phase susceptibility has been observed in external magnetic field (Bdc = 0.1 T) revealing the following parameters of slow relaxation of magnetization for 1: energy of the spin reversal barrier, Ueff = 16.0 cm-1 (Ueff/kB = 23.0 K) and the relaxation time, τ0 = 1.28 × 10-6 s. In the case of complex 2, no maxima of frequency dependent out-of-phase susceptibility have been observed and thus, the value of Ueff = 17 cm-1 has been estimated using the expression Ueff = |D| × (S2 - 1/4). It has been demonstrated that the degree of substitution and the type of substituents on the pyridyl moieties of the tripodal ligands (L1 and L2) used in these penta-coordinate cobalt(ii) complexes have significant impact on structural and magnetic features.