ABSTRACT Vibration-based fault diagnosis from rotary machinery requires prior feature extraction, feature selection, or dimensionality reduction. Feature extraction is tedious, and computationally expensive. Feature selection presents unique challenges intrinsic to the method adopted. Nonlinear dimensionality reduction may be achieved through kernel transformations, however there is often a trade-off in information to achieve this. Given the above, this study proposes a novel autoencoder (AE) pre-processing framework for vibration-based fault diagnosis in wind turbine (WT) gearboxes. In this study, AEs are used to learn the features of WT gearbox vibration data while simultaneously compressing the data, obviating the need for costly feature engineering and dimensionality reduction. The effectiveness of the proposed framework was evaluated by training genetically optimized linear discriminant analysis (LDA), multilayer perceptron (MLP), and random forest (RF) models, with the AE’s latent space features. The models were evaluated using known classification metrics. The results showed that the performance of the models depends on the size of the AE’s latent space. As the size of the AE’s latent space increased, the quality of features extracted improved until a plateau was observed at a latent space dimension of 10. The AE pre-processed genetically optimized RF, MLP, and LDA models, designated AE-Pre-GO-RF, AE-Pre-GO-MLP, and AE-Pre-GO-LDA, were evaluated for accuracy, sensitivity, and specificity in the classification of seven (7) gearbox fault conditions. The AE-Pre-GO-RF model outperformed its counterparts, scoring 100% for all evaluated metrics, though with the longest training time (239.50 sec). Comparable results were found comparing this study with similar investigations involving traditional vibration processing techniques. More so, it was established that effective fault diagnosis of the WT gearbox can be achieved through manifold learning with AEs without expensive feature engineering.