Heritage science is a broad and interdisciplinary scientific field that focuses on the characterization of materials, techniques, deterioration processes, and the preservation of cultural assets. This field encompasses a wide array of subjects and places particular emphasis on the investigation of complex and heterogeneous materials—such as textiles, paintings, architectural structures, as well as human and fossil remains—all of which contribute collectively to the reconstruction of the past and the deepening of our historical understanding through time. Over time, all materials are influenced by environmental factors, and their interactions with surrounding conditions can lead to alterations driven by chemical, physical, and biological processes. Among these materials, organic components—particularly proteinaceous compounds—play a pivotal role. In prehistoric archaeology and geological contexts, proteins provide valuable insights into ancient diets, health status, and even evolutionary adaptations. In the context of artworks, the analysis of proteins can reveal important information regarding production techniques, fabrication processes, and restoration strategies. Furthermore, protein studies offer clues that help improve our understanding of past cultural practices. Due to their low abundance, interaction with mineral matrices, and continuous degradation, the development of analytical methods that both aid in sample preservation and enhance our understanding of degradation mechanisms is essential. Such research forms the foundation of advancements in cultural heritage conservation science and is crucial for ensuring the longevity and structural integrity of historical objects. The aim of this study is to provide a concise overview of the importance of investigating historical proteinaceous materials and to explore recent approaches in their recovery, identification, and analysis. This work seeks to highlight the role of proteins as valuable informational resources in the fields of archaeology, art conservation, and biogeo-heritage.