Targeted protein degradation (TPD) strategies, including BET inhibitors and PROTACs, offer a promising approach for cancer therapy by selectively degrading disease-relevant proteins. However, their clinical translation is hindered by poor solubility, potential systemic toxicity, and suboptimal delivery. Here, we evaluate the feasibility of natural tuna collagen-based hydrogels as biocompatible and biodegradable carriers for localized delivery of the BET inhibitor JQ1 and its PROTAC derivative MZ1 in breast cancer. Hydrogel formulations were systematically optimized by analyzing drug encapsulation, internal fiber structure, and drug-matrix interactions, which influenced release kinetics and administration pathways. Physicochemical characterization confirmed collagen structural integrity, injectability, and mechanical stability. In vitro studies in three breast cancer cell lines showed that hydrogel-encapsulated drugs retained therapeutic efficacy and effectively inhibited migration. Cell cycle arrest and apoptosis assays, together with Synchrotron FTIR microspectroscopy, confirmed preservation of the drugs' mechanisms of action. To our knowledge, this is the first study integrating JQ1 and MZ1 into a natural gelatin-based hydrogel system for localized cancer therapy, providing a foundation for in vivo evaluation and potential applications in advanced drug delivery, tissue engineering, and precision medicine.