Chlorhexidine digluconate (CHX) has demonstrated notable potential in minimizing inflammation and marginal bone loss (MBL) at 1-year evaluations; however, evidence regarding its sustained effectiveness on peri-implant stability remains scarce. This study aimed to assess the extended effects (5-year follow-up) of a placebo gel (Group A: 16 patients) versus a 0.20% CHX gel (Group B: 15 patients), both applied during all previous surgical and prosthetic procedures. Follow-up assessments were carried out in 2022, including biological, clinical, and radiographic evaluations. Statistical analyses were performed. Across five years, implant success reached 96.7%, while 41.9% of participants failed to attend their yearly oral hygiene appointments. Mean MBL measured 1.04 ± 0.39 mm, showing no statistically significant difference between the two groups. Importantly, patients who consistently attended maintenance visits exhibited significantly lower MBL values compared to those who did not (p < 0.05). After 5 years, CHX’s direct impact was no longer evident, with both cohorts exhibiting moderate bone loss. Nonetheless, findings indicate that initial decontamination procedures may improve both short- and long-term results. Patients who initially experienced less MBL due to CHX use maintained this advantage even after 5 years. Furthermore, the study highlights the crucial role of annual check-ups in preventing and managing biological issues at an early stage.