Ultrashort self-assembling peptides of typically less than 5 amino acids in length can be modified with highly aromatic protecting groups such as Fluorenylmethyloxycarbonyl (Fmoc) resulting in the rapid formation of nanofibrillar hydrogels. These hydrogels show great promise as scaffolds for tissue engineering and 3D cell culture. If further modified with bioactive peptide sequences, the hydrogels can be used to promote and control cell adhesion, and even support the ability for cultured mesenchymal stem cells (MSCs) to differentiate into therapeutically useful lineages, such as chondrocytes. Whilst there have been numerous examples of how the addition of such sequences can promote the bioactivity of cultured cells, the effect adding these sequences has on the nanoarchitecture, mechanical properties and stability of the resultant hydrogels is less well explored. Here, we have performed a series of experiments investigating the effect incorporating stoichiometric amounts of Fmoc-Arg-Gly-Asp (Fmoc-RGD) into Fmoc-Phe-Phe (Fmoc-FF) hydrogels has on nanofibril morphology, and the rheological properties and stability of the formed gels. Furthermore, we correlate these variations in nano-architectural and mechanical properties with their ability to support the culture of clinically valuable bone marrow derived human mesenchymal stem cells (hMSCs). Our results show that at relatively low concentrations Fmoc-RGD is incorporated into the self-assembled Fmoc-FF nanofibrils creating biocompatible hydrogels capable of supporting hMSC growth for up to a week. At increased concentrations of Fmoc-RGD, incorporation into the nanofibrils is lost and the hydrogels that form are no longer stable enough to support the culture of hMSCs for multiple days. These findings shed light on the importance of balancing the positive effects of adding bioactive ligands to 3D scaffolds with the negative effects these ligands can have on the stability and mechanical properties of these scaffolds. Further, the findings will have implications for the choice of ultrashort peptide scaffolds for tissue engineering applications to support MSCs towards chondrogenic differentiation, and their application as gel-cell constructs in cartilage tissue engineering for osteoarthritis.