Self-assembly is a nature inspired novel engineering tool to build functional new generation of adaptable and complex biomaterials with variety of chemical and physical properties based on recent discoveries at the interface of chemistry, biology and materials science. Within self-assembling building blocks, peptides consisting natural amino acids and possibilities to integrate other molecules via synthetic approaches are intriguing biomacromolecules to obtain dynamic architectures at both nano and bulk scales for biomedical applications. In this thesis, the development of novel biomaterials through molecular self-assembly of the biomimetic peptides, bioactive peptide amphiphiles and their composite architectures with polymeric system for biomedical applications were presented. In the first chapter, the concept of self-assembly, design principles of the self-assembling peptide based building blocks and advanced characterization techniques for these materials were discussed to provide general perspective on the field. The applications of peptide based biomaterials with an emphasis on the drug delivery and regenerative medicine purposes were also highlighted in this part. In the second chapter, amyloid inspired self-assembling peptides and their supramolecular assemblies were presented in the context of developing nature-inspired biocompatible and mechanically stable supramolecular peptide based biomaterials. In the third chapter, supramolecular PA nanofiber gels which can form supramolecular nanofibrous networks at physiological conditions and encapsulate chemotherapeutics with high efficacy were examined as controlled local drug delivery system at both in vitro and in vivo conditions. In the fourth chapter, the facile fabrication strategy to create a novel self-assembled peptide amphiphile (PA) nanofibers and PEG composite hydrogel system as synthetic ECM analogues was discussed. It was showed that the synergistic combination of different classes of materials provide us new opportunities to develop biomaterials with independently tunable biochemical, mechanical and physical properties.