Peptide-based materials represent a rapidly growing field in nanotechnology, bridging bottom-up self-assembly and top-down approaches for the development of functional nanostructures. Among these systems, peptide-based nanogels (NGs), namely nanogels in which peptides assume a structural role, have emerged as a promising class of injectable formulations. Typically characterized by a core–shell architecture, these systems are closely related to peptide hydrogels in terms of structural organization. This review provides a state-of-the-art overview of peptides used as core structural elements for NG formulation, focusing on the peptide building blocks employed, the main formulation methodologies, and their current applications, with particular emphasis on pharmaceutical ones. Their potential as drug delivery systems and stimuli-responsive platforms for controlled and targeted release is also reported. For clarity, the reported formulations are classified according to the chemical nature of the core-structuration peptide, distinguishing systems based on Fmoc-FF from those derived from other primary sequences, including Boc-protected tripeptides, dehydropeptides, and chemically crosslinked peptide assemblies.