Alginate decoration with more than one type of biomolecule is becoming a prevalent process in the pursuit to turn alginate hydrogels into synthetic extracellular matrices (ECMs). Here we present a systematic study of the structural–physical properties–function relationship of alginate–G4RGDY–heparin aqueous solutions and hydrogels. Small-angle X-ray scattering (SAXS) and rheology were used to characterize the systems’ nanostructure, viscosity of the solutions, and storage modulus of the hydrogels. The bioactivity of these gels was explored by evaluating their ability to sustain the release of vascular endothelial growth factor (VEGF). We show that the mode and order of conjugating the heparin and the peptide to the alginate backbone greatly affect the modified alginate hydrogels’ structure–properties–function relations. Moreover, we show that a detailed structural analysis of the conjugated architecture in solution can be used as a tool to adapt the properties of alginate–heparin–peptide hybrid hydrogels.