This paper presents the proposal of a method to recognize emotional states through EEG analysis. The novelty of this work lies in its feature improvement strategy, based on multiclass genetic programming with multidimensional populations (M3GP), which builds features by implementing an evolutionary technique that selects, combines, deletes, and constructs the most suitable features to ease the classification process of the learning method. In this way, the problem data can be mapped into a more favorable search space that best defines each class. After implementing the M3GP, the results showed an increment of 14.76% in the recognition rate without changing any settings in the learning method. The tests were performed on a biometric EEG dataset (BED), designed to evoke emotions and record the cerebral cortex’s electrical response; this dataset implements a low cost device to collect the EEG signals, allowing greater viability for the application of the results. The proposed methodology achieves a mean classification rate of 92.1%, and simplifies the feature management process by increasing the separability of the spectral features.