Artificial intelligence (AI), particularly deep learning (DL) and machine learning (ML) have revolutionized disease diagnosis using complex medical images such as X-rays and CT scans, significantly improving accuracy in identifying various medical conditions. However, concerns arise regarding the trustworthiness of these models due to their vulnerability to adversarial attacks, potentially leading to inaccurate predictions. In response, we propose an innovative pipeline defensive approach that integrates denoising techniques like Total Variation Minimization (TVM) and Non-local (NL) means, followed by a fuzzy logic-based image transformer called Fuzzy Image Transformations (FIT). Deployed during the inferencing phase as a preprocessing module, this strategy aims to fortify DL medical diagnosis models, addressing adversarial vulnerabilities and ensuring their reliability in critical healthcare applications. Our focus is narrowed down to COVID-19 diagnosis, where we initially developed a model for accurately classifying lung CT images, covering both normal and COVID-19 pneumonia cases. Our experimental procedures, employing the Stratified K-Fold cross-validation method with K=5, systematically evaluate the model’s susceptibility to benchmark adversarial attacks such as the Fast Gradient Sign Method (FGSM), revealing a significant drop in aggregate average metrics across all folds under adversarial conditions. Specifically, precision (P), recall (R), accuracy (A), and F1-score (F) metrics decrease from 95.86 %, 96.16 %, 95.85 %, and 96.00–12.54 %, 13.13 %, 12.63 %, and 12.83 %, respectively. Notably, our proposed pipeline defense approach demonstrates substantial efficacy in enhancing diagnostic models, with average P, R, A, and F metrics improving impressively to 92.65 %, 92.39 %, 92.65 %, and 92.51 %, respectively, when applied to the same adversarial images. These promising results underscore the potential of our proposed pipeline defense techniques to enhance the resilience and reliability of AI-based diagnostic systems.