(1) Background: This study evaluates the effects of photobiomodulation (PBM) therapy on the peri-implant bone healing of implants with a machined surface (MS) and treated surface (TS). (2) Methods: Topographic characterization of the surfaces (scanning electron microscopy [SEM]- energy dispersive X-ray spectroscopy [EDX]) was performed before and after implant removal. Twenty rabbits were randomly divided into four groups: MS and TS groups (without PBM therapy) and LMS and LTS groups (with PBM therapy). After implant placement, the stability coefficient (ISQ) was measured. In the periods of 21 and 42 days, the ISQ was measured again, followed by biomechanical analysis. (3) Results: The surfaces of the TS implants showed topographic differences compared with MS implants. The ISQ values of the LMS were statistically significant when compared with those of the MS at 42 days (p < 0.001). The removal torque values of the LMS were statistically significant when compared with those of the MS at 21 days (p = 0.023) and 42 days (p = 0.023). For SEM, in general, the LMS, TS and LTS presented high bone tissue coverage when compared to MS. (4) Conclusions: The PBM therapy modulated the osseointegration process and was evidenced mainly on the machined surface.