Functionalized biomaterials interface with tissue upon implantation. There is a growing need to understand how materials properties influence this interaction so that efficient tissue engineering systems can be developed. In this study, we characterize collagen organization in response to functionalized glass beads implanted in SKH1-E mice. Poly-l-arginine (PLR) was modified with arginine derivatives to create a functionalized surface and was coated on glass beads. Tissue sections were removed 28 days post-implantation and were imaged using second harmonic generation (SHG) microscopy. These chemical modifications were able to alter the collagen distribution from highly aligned to disordered (17 ± 6 to 78 ± 1° full width at half-maximum (FWHM)) and the collagen III/I ratio (0.02 to 0.42). Principal component analysis (PCA) comparing the physical properties of the modifiers (e.g. hydrophobicity, molar volume, freely rotating bonds, polarizability) with the SHG analytically derived parameters (e.g. collagen III/I ratio, collagen orientation) was performed. Chemical properties of the PLR-like modifications including lipophilicity, along with the number of freely rotating bonds and the polarizability had significant effects on the collagen surrounding the implant, both in terms of collagen orientation as well as the production of collagen III. These findings demonstrate the possibility of tuning the foreign body response, in terms of collagen deposition and organization, to positively influence the acceptance of implanted biomaterials.