Purpose: To compare and evaluate the effect of flap and flapless implant placement on peri-implant hard and soft tissue health. Materials and methods: A total of 40 implant sites in the mandibular molar region in 40 patients were chosen, with 20 for the conventional flap procedure and 20 for the flapless procedure. The parameters selected were radiographic marginal bone loss, implant mobility, modified plaque index, modified bleeding index (MBI), and probing depth measurement at the time of loading (baseline), 3, 6, and 12 months after loading. Descriptive statistics and repeated measures of analysis of variance (ANOVA) tests were done to evaluate significant differences at different time intervals. Results: The flapped technique showed higher mesial and distal crestal bone loss at 3, 6, and 12 months (p = 0.001). The bleeding index was also higher in flapped implants at 3, 6, and 12 months (p = 0.002). Probing depth was significant for flapped implants on all sides at different intervals (p-values ranging from 0.001 to 0.024). The plaque index was not significant. The mobility index was 0 ± 0 for both techniques after 12 months, with significant p-values of 0.025 and 0.001 for flapless and flapped techniques, respectively. Conclusion: Marginal bone loss is lower in flapless implant surgical placement. No clinically significant difference was observed between flap and flapless surgery in terms of implant mobility and plaque index. The probing depth and bleeding index around implants placed using the flap technique showed significant changes compared to the flapless technique.