Diarrhea is a globally major problem especially Escherichia coli induced diarrhea becoming fatal nowadays in developing countries. Colon-targeted chitosan microspheres (Ms) comprising of lipase‑zinc and lipase‑copper complexes were prepared, loaded with Attapulgite (Cts-Li-Zn-ATG/Ms and Cts-Li-Cu-ATG/Ms) for the treatment of bacterial diarrhea. Thin layer chromatography (TLC) and Fourier-transform infrared spectroscopy (FTIR) studies were used for confirmation of proposed lipase-metal complexes. Ms showed particle size range 18 ± 0.24 to 23 ± 0.83 μm, zeta potential −13.7 ± 0.71 to −29.3 ± 1.34 mV, PDI 0.5 ± 0.04 to 1.0 ± 0.07 and hemolytic activity was found to be <5 ± 1.25 %. After coating with Eudragit S-100 for colon targeting, in-vitro % drug release of ATG at pH 7.4 was 80 ± 0.21 % for Eud-Cts-Li-Zn-ATG/Ms while it was increased to 83 ± 0.54 % for Eud-Cts-Li-Cu-ATG/Ms within 7 h, respectively. In-vivo anti-diarrheal activity of Eud-Cts-Li-Zn-ATG/Ms and Eud-Cts-Li-Cu-ATG/Ms was performed by oral challenge on albino mice having infectious diarrhea colonized with E. coli. Results revealed significant anti-diarrheal effect of proposed Eud-Cts-Li-Cu-ATG/Ms in terms of weight gain from 24 ± 0.12 g to 26.05 ± 0.31 g, which was 2-fold increase as compared to Eud-Cts-Li-Zn-ATG/Ms. Conclusively, Eud-Cts-Li-Cu-ATG/Ms provides an innovative alternate for the treatment of bacterial diarrhea with additional support of chitosan and lipase for nutritional support and immunity which was compromised in diarrheal patients.