We construct a phase diagram for self-assembling biologically active peptide amphiphiles. The structure and stability of the assemblies are studied as a function of pH and salinity of the solution. The general features of the phase diagram are predicted based on theoretical modeling of the self-assembly process, as well as experimental data, and further experiments are performed to verify and ascertain the boundary locations of the diagram. Depending on solution conditions, the amphiphiles can form cylindrical or spherical micelles, intermediate structures between these, or may not assemble at all. We also demonstrate that changing conditions may result in phase transitions among these structures. This type of phase diagram could be useful in the design of certain supramolecular nanostructures by providing information on the necessary conditions to form them.