In this study, Density Functional Theory and the Boltzmann transport equation are applied to calculate the semiclassical thermoelectric transport properties of phthalocyanine (PC) covalent organic frameworks with different central metals in the macrocycle MPc-COFs, (M = Co, Cu, and Zn), which have a slipped-AA stacking of 2D polymer sheets. The weakening of π-π stacking increased the role of in-plane intramolecular through-bond carrier transfer involving σ/π interactions, leading to significant anisotropy of transport coefficients in the studied compounds, which are also affected by the nature of the transition metals. The maximum values of thermopower for Co-Pc COF (770 μV/K) and Cu-Pc COF (− 423 μV/K) were found along the in-plane direction. However, for ZnPc-COF, the maximum positive value of the Seebeck coefficient (156 μV/K) was found along the stacking direction, while the maximum value of the thermopower along the in-plane direction was equal to − 315 μV/K. The electronic fitness function was calculated to estimate the thermoelectric performance of the studied compounds for both p- and n-type doping at 300 and 800 K. The maximum values of the electronic fitness function are observed for Cu-Pc and Zn-Pc COFs along the stacking direction at 800 K for both p- and n-type doping, while for p-doped Co-Pc COF the maximum value of this function was found along the in-plane direction.