A new synthetic route was carried out via a one-pot reaction to prepare a novel series of amidine/amidinate cobalt complexes 8-10 by mixing ligand 2 (6-pyridin-2-yl-[1,3,5]-triazine-2,4-diamine) with Co(II) in acetonitrile or benzonitrile. We observed that a change of solvent from methanol (used in complex 7, previously reported) to nitrile solvents (MeCN and PhCN) led to the in situ incorporation of the amidine group, ultimately forming 8-10. So far, this is a unique method reported to introduce amidine/amidinate groups into a pyridinyl-substituted diaminotriazine complex. Remarkably, the single crystal X-ray diffraction study (SCXRD) of these new compounds reveals associations involving Janus DAT amidine and Janus DAT amidinate. A mechanism is proposed to explain the formation of amidine/amidinate groups by investigating the single crystal structures of the possible intermediates 11 and 12 where the cobalt ion acts as a template. These amidine/amidinate cobalt complexes were used as a model to assess the photocatalytic activity for the hydrogen evolution reaction (HER). Complexes 9 and 10 show a 74% and 86% enhancement, respectively, of the catalytic activity towards the HER compared to complex 7. This highlights the structure-property relationship. By examining the novel cobalt complexes described here, we discovered the following: (i) a method to introduce an amidine group into a pyridine DAT-based complex, (ii) the efficiency of amidine complexes to form multiple hydrogen bonds to direct the molecular organization, (iii) the plausible mechanism of formation of amidines based on the SCXRD study, (iv) the modification of the final structure and hence the final properties by varying the reaction conditions, and (v) the utility of amidine complexes towards photocatalytic HER activity.