Zeolites are effective adsorbents to remove heavy metals from aqueous solutions. To investigate the role of the template on enhancing the ability of zeolites to absorb metals, methionine amino acid was introduced to zeolite synthesis gel to produce a modified analcime zeolite. Afterwards, adsorption of Cu(II) and Ni(II) cations on templatefree analcime and methionine-templated analcime were studied and the experimental data were fitted with Freundlich and Langmuir equations in order to obtain the sorption parameters. Batch experiments were carried out to evaluate Cu(II) and Ni(II) adsorption at different pH values, heavy metals concentrations, and removal intervals. The results showed that the metal removal efficiency was strongly dependent on the pH of the solutions. The analcime zeolites absorbed Cu(II) more readily than Ni(II). Furthermore, methionine-templated analcime exhibited a higher potential for heavy metal removal than the template-free zeolite. Raman spectra indicated that the presence of a methionine template during analcime zeolite synthesis could create a complex structure of Cu−S (methionine)/zeolite and Ni−S (methionine)/zeolite. Thus introducing a sulphur-containing template such as methionine may give further possibilities to improve the metal removal efficiency of zeolites.