Three different metal-containing zinc phosphate, [C3H12N2][Zn0.5Fe1.5(PO4)2] (1), [C3H12N2][Zn0.67Co1.33(PO4)2] (2) and [C3H12N2][Zn0.67Ni1.33(PO4)2] (3) with EDI topology were prepared by sol–gel assisted hydrothermal method. The advantages of this method are lower synthesis temperature and uniform mixing. The crystalline metal-containing zinc phosphate zeolites exhibit a variety of SEM morphologies because of the entanglement of three different metal ions. The zinc ions in the zinc phosphate EDI molecular sieve were partially substituted by Fe, Co and Ni ions. The ICP analysis shows that the metal ratios of Zn/M are 1/3, 1/2 and 1/2. Variable temperature susceptibility was measured on powder samples in the range 2–300 K. All three M-EDI molecular sieves exhibit antiferromagnetic properties. In addition, they were analyzed by XRD, CHN, IR and TG.