The browning process of food products if often formed upon cutting and damage during their processing, transport, and storage, amongst other potential sources and reasons. Enzymic browning can be mainly due to polyphenol oxidase (PPO) and peroxidase (POD) enzymes. Visible/near-infrared (Vis/NIR) imaging spectroscopy in the range of 350–1150 nm was used in this study for automatic and non-destructive evaluation of PPO and POD activity levels in three bell pepper varieties (red, yellow, orange; N = 30), with a total of 30 inputs samples in each variety. The spectral data were then modeled by the partial least squares regression (PLSR) throughout the whole spectral range, without using any subset of the most effective wavelength (EW) values. Regression determination coefficient (R2) values for the estimation (prediction) of POD enzyme activity levels were 0.794, 0.772, and 0.726 for red, yellow, and orange bell peppers, respectively, all over the validation set. At the same time, the activity levels of PPO enzyme over bell peppers showed R2 values of 0.901, 0.810, and 0.859, for red, yellow, and orange bell peppers, respectively, all over the validation set. In addition, a combination of support vector machine (SVM) with either genetic algorithms (GA), particle swarm optimization (PSO), ant colony optimization (ACO), or imperialistic competitive algorithms (ICA) hybrid machine learning (ML) techniques were used to select the optimal (discriminant) spectral EW wavelength values, and regression performance was consistently improved, to judge from higher regression fit R2 values. Either 14 or 15 EWs were computed and selected in order of their discriminative power using previously mentioned ML techniques. The hybrid SVM-PSO method resulted the best one in the process of selecting the most effective wavelength values (nm). On the other hand, three regression methods comprising PLSR, multiple least regression (MLR), and neural network (NN), were employed to model the SVM-PSO selected EWs. The ratio of performance to deviation (RPD), the R2 and the root mean square error (RMSE), over the test set, for the non-linear NN regression method exhibited better results as compared to the other two regression methods, being closely followed by PLSR, and therefore NN regression method was selected as the best approach for modeling the most effective spectral wavelength values in this study.