This work presents, for the first time, a fast and highly sensitive electrochemical method for determination of three organophosphorus compounds (OPs), diazinon (DZN), malathion (MLT), and chlorpyrifos (CLPF), using a modified pyrolytic graphite electrode (PGE) coupled to batch injection analysis system with multiple pulse amperometric detection (BIA–MPA). The PGE was modified by a nanocomposite based on functionalized carbon nanotubes (CNTf) and silver nanoparticles (AgNPs). The OPs samples were directly analyzed on the modified working electrode surface by BIA-MPA system in Britton-Robinson (BR) buffer 0.15 mol L⁻¹ at pH 6.0. The MPA detection of DZN, MLT and CLPF was performed using two potential pulses, which were sequentially applied on modified PGE at −1.3 V (100 ms) and +0.8 V (100 ms) for selective determination of these three OPs and working electrode cleaning, respectively. Under optimized conditions, the sensor presented a linear range of 0.1–20 μmol L⁻¹ for DZN, 1.0–30 μmol L⁻¹ for MLT and from 0.25 to 50 μmol L⁻¹ for CLPF. The limits of detection (LOD) and quantification (LOQ) of 0.35 and 1.18 μmol L⁻¹ for DZN, 0.89 and 2.98 μmol L⁻¹ for MLT, and 0.53 and 1.78 μmol L⁻¹ for CLPF were obtained. The proposed method exhibited high sensitivity of 0.068, 0.030 and 0.043 mA L μmol⁻¹ for DZN, MLT and CLPF detection, respectively. Furthermore, the BIA-MPA system provided an analytical frequency of 71 determinations per hour for direct determination of these OPs in water and food samples. The modified PGE coupled to BIA-MPA system showed a high stability of electrochemical response for OPs detection with relative standard deviation (RSD) of 1.60% (n = 20). The addition-recovery studies of the proposed method were carried out in tap water, orange juice, and apple fruit real samples, which showed suitable recovery values between 77 and 124%. The analytical performance of the developed sensor provides an attractive alternative method for OPs determination with great potential for a fast and sensitive application in contaminated samples with these pesticides.