In this study, a polymer-based surface plasmon resonance (SPR) sensor for refractive index measurements was designed and manufactured via inkjet 3D printing; then, it was optically characterized. Next, it was investigated how the surface finish of the 3D printed optical waveguide affects the sensor performance, i.e., its sensitivity. More in detail, it was studied how the surface roughness changes with the placement of the 3D printed items on the building platform. To achieve this purpose, a Phase I distribution-free quality monitoring analysis of the selected manufacturing process was implemented for a small pilot production run. The aim was to check the stability of surface roughness versus the placement of the 3D printed parts on the building platform. The 3D printed sensor’s surface roughness was assessed through a profilometry study. In particular, the surface roughness was determined for the core of the optical waveguide used to excite the SPR phenomena. Furthermore, the SPR sensors were optically characterized to find the existing relationship between their sensitivity and the considered quality of surface finish. In particular, by varying the surface roughness of the used waveguide, the light scattering in the waveguide changes, and the SPR sensitivity changes too, similarly to the light-diffusing fibers covered by gold nanofilms where the guided light is scattered through a plurality of voids distributed in the core. The procedure followed to investigate the sensor roughness, and establishing their performance enabled the optimal operative range for their application in practice to be identified. Finally, a better knowledge of the 3D printing manufacturing process has been achieved to improve quality of surface finish.