Condition monitoring (CM) is essential for maintaining operational reliability and safety in complex machinery, particularly in robotic systems. Despite the potential of deep learning (DL) in CM, its ‘black box’ nature restricts its broader adoption, especially in mission-critical applications. Addressing this challenge, our research introduces a robust, four-phase framework explicitly designed for DL-based CM in robotic systems. (1) Feature extraction utilizes advanced Fourier and wavelet transformations to enhance both the model’s accuracy and explainability. (2) Fault diagnosis employs a specialized Convolutional Long Short-Term Memory (CLSTM) model, trained on the features to classify signals effectively. (3) Model refinement uses SHAP (SHapley Additive exPlanation) values for pruning nonessential features, thereby simplifying the model and reducing data dimensionality. (4) CM interpretation develops a system offering insightful explanations of the model’s decision-making process for operators. This framework is rigorously evaluated against five existing fault diagnosis architectures, utilizing two distinct datasets: one involving torque measurements from a robotic arm for safety assessment and another capturing vibration signals from an electric motor with multiple fault types. The results affirm our framework’s superior optimization, reduced training and inference times, and effectiveness in transparently visualizing fault patterns.