The extension of neurites on 2D collagen-coated substrates and within 3D collagen gels is based on various chemical and mechanical environmental factors. However, extrapolating results from 2D studies to 3D environments are difficult, especially with regard to neural outgrowth. The aim of this study was to investigate the effects of inhibitory molecules on nerve growth in 3D environments as compared to 2D surfaces. E9 chick dorsal root ganglion cells were seeded within collagen gels as well as onto collagen-coated glass and were exposed, for 24 h, to one of three experimental peptide sequences; arginine-glycine-aspartic acid-threonine (RGDT), cyclo(RGD-D-Phe-Val) (cRGD), or aspartic acid-glycine-glutamic acid-alanine (DGEA). In 3D collagen gels, only the cRGD peptide sequence reduced neurite extension across a variety of gel concentrations. In contrast, on 2D surfaces, both RGD peptides reduced the number of cells expressing neurites, but cRGD still exhibited superior inhibition of neurite expression. Further evaluation of cRGD results revealed that the peptide altered neurite growth vs. stiffness to a more linear relationship that is more typical of non-adhesive environments. Overall, these results further demonstrate the importance of peptide confirmation and sequence when investigating cell behavior in 3D environments.