Developing effective material for pesticide adsorption is a vital issue to protect the environment from their harmful effects. Copper-based metal–organic frameworks including Cu-BTC and its mixed metal derivatives (Fe-Cu-BTC, Co–Cu-BTC, and Mn-Cu-BTC) were successfully formed. Fe-Cu-BTC, Co–Cu-BTC and Mn-Cu-BTC MOFs were synthesized by direct substituting one Cu atom in Cu-BTC with Fe, Co, or Mn. Their structures were characterized using Powder X-ray diffraction (PXRD), Fourier-transform infrared spectroscopy FTIR, scanning electron microscopy with EDX, Transmission electron microscopy, BET surface area analysis, and Size distribution. Prepared MOFs adsorbed chlorpyrifos from wastewater and their adsorption capacities were compared. Pseudo-second-order kinetics and Langmuir isothermal models were the best to describe the adsorption of chlorpyrifos from water. The coordination bonding was the dominant mechanism; physical adsorption, π-π stacking interaction, and hydrogen bonding were also participated in the adsorption process. Cu-BTC, Fe-Cu-BTC, Co–Cu-BTC and Mn-Cu-BTC had elimination capacities of 379, 851, 683, and 762 mg/g, respectively. This study also investigates their antimicrobial activity against gram-positive and gram-negative bacteria and they exhibited a good inhibition effect. The inhibition zone of Co–Cu-BTC is greater than Cu-BTC with 1.44, 1.38, and 1.60 times for E. coli, Ps. Aeruginosa, S. aureus, respectively. The synthesized MOFs are promising materials for the removal of chlorpyrifos with effective antimicrobial agents.