Medical foundation models are gaining prominence in the medical community for their ability to derive general representations from extensive collections of medical image-text pairs. Recent research indicates that these models are susceptible to backdoor attacks, which allow them to classify clean images accurately but fail when specific triggers are introduced. However, traditional backdoor attacks necessitate a considerable amount of additional data to maliciously pre-train a model. This requirement is often impractical in medical imaging applications due to the usual scarcity of data. Inspired by the latest developments in learnable prompts, this work introduces a method to embed a backdoor into the medical foundation model during the prompt learning phase. By incorporating learnable prompts within the text encoder and introducing imperceptible learnable noise trigger to the input images, we exploit the full capabilities of the medical foundation models (MedFM). Our method requires only a minimal subset of data to adjust the text prompts for downstream tasks, enabling the creation of an effective backdoor attack. Through extensive experiments with four medical foundation models, each pre-trained on different modalities and evaluated across six downstream datasets, we demonstrate the efficacy of our approach. Code is available at https://github.com/asif-hanif/baple.