The design of electrochemical sensors is crucial considering important factors such as efficiency, low cost, biocompatibility, and availability. Manganese oxides are readily available, low-cost, and biocompatible materials, but their low conductivity limits their efficiency as sensors. Today, morphology engineering of manganese oxide has been one of the most common research topics, because manganese oxides’ electrochemical properties are highly dependent on their morphologies. In this study, a method for reducing the charge transfer resistance (Rct) of MnO2-based electrodes was established by the cyclic voltammetry technique accompanied by step-by-step heat treatment to electrodeposition MnO2 nanofilm, which remarkably improved the Rct. Next, the sensing performance of MnO2/FTO for two separate measurements was examined, one for the simultaneous measurement of paracetamol (PAR) and 4-aminophenol (4-APh), and the other for the measurement of 4-nitrophenol (4-NP). Under the optimum conditions, the linear ranges of 4-APh, PAR, and 4-NP, were 0.8 to 22.0 µM, 2.0 to 55.0 µM, and 0.1–250 µM, with limits of detection (LOD) of 0.19 µM, 0.60 µM, and 0.01 µM, respectively. It also was unaffected by a 200-fold excess of interferences. In addition, the designed sensor was successfully applied to the analysis of real samples.