In this work, chemometrics and electrochemistry connected to each other to open a new way for assisting food industry specialists based on developing a novel electrochemical sensor for simultaneous determination of malathion (MT) and diazinon (DZ) in the presence of patulin (PT) and citrinin (CT) as uncalibrated interference in fruit juices. The sensor was fabricated based on modification of a glassy carbon electrode (GCE) by chitosan-ionic liquid (Ch-IL), electrodeposition of gold nanoparticles (Au NPs), drop-casting of multiwalled carbon nanotubes-IL (MWCNTs-IL), and electrochemical synthesis of dual templates molecularly imprinted polymers (DTMIPs) in which MT and DZ were used as templates. Effects of experimental variables on structure and response of the sensor were screened and optimized by Min Run screening and central composite design, respectively. After optimization, the third-order hydrodynamic differential pulse voltammetric (HDPV) data were generated based on changing modulation times and modulation amplitudes as instrumental parameters and modeled by N-PLS/RTL, U-PLS/RTL, U-PCA/RTL, APARAFAC, PARAFAC2 and MCR-ALS to select the best one to assist the sensor for ultra selective simultaneous determination of MT and DZ in the presence of PT and CT as uncalibrated interference in fruit samples. The results confirmed the MCR-ALS was the best assistance for DTMIPs/MWCNTs-IL/Au NPs/Ch-IL/GCE for simultaneous determination of MT and DZ in the presence of PT and CT as uncalibrated interference in both synthetic and real samples. Performance of the sensor assisted by MCR-ALS for ultra selective simultaneous determination of MT (0.1 pM–12.5 pM, LOD = 0.01 pM) and DZ (0.25 pM–8.5 pM, LOD = 0.15 pM) was really admirable which was comparable with HPLC with UV detection while it was faster, simpler and low-cost in comparison to HPLC-UV which motivated us to introduce it as a reliable method to assist food industry specialists for quality assurance purposes.