We present a novel and practical deep learning pipeline termed RandomForestMLP. This core trainable classification engine consists of a convolutional neural network backbone followed by an ensemble-based multi-layer perceptrons core for the classification task. It is designed in the context of self and semi-supervised learning tasks to avoid overfitting while training on very small datasets. The paper details the architecture of the RandomForestMLP and present different strategies for neural network decision aggregation. Then, it assesses its robustness to overfitting when trained on realistic image datasets and compares its classification performance with existing regular classifiers.