Zinc linked amino acid complex, Zn(l‐proline)2, is considered as a green catalyst for the synthesis of novel series of pyrimidine derivatives 5a–q. The pyrimidines 5a–q were prepared via two pathways: the first is a one‐pot reaction of guanidines 3a–c with aromatic aldehyde 1 and acetophenones 2; and the second one is the reaction of guanidines 3a–c with different chalcones 4a–j in aqueous medium. The simplicity of the operation, the short reaction time, and the high efficiency (97%) are the main advantages of this protocol. Furthermore, the green aspects of this synthetic protocol were further investigated by examining the reusability of Zn(l‐proline)2 complex throughout five consecutive cycles without a significant loss of catalytic activity. This new procedure has presented remarkable advantages in terms of safety, simplicity, stability, mild conditions, a short reaction time, excellent yields, and high purities without using any organic solvents.