Background: Dental implants are considered better, latest, and most advanced technique of teeth replacement in present times with more teeth loss and increased related concerns. Aims: The present clinical trial was carried out to assess marginal bone loss and implant failure in immediate and delayed loading implants. The study also evaluated healing using Polymerase Chain Reaction (PCR) and the effect of risk factors on marginal bone loss. Materials and Methods: The 44 subjects were randomly divided into two groups with immediate loading and delayed loading protocols. Various soft-tissue parameters were seen clinically. Quantitative PCR was done to detect biomarkers. The collected data were subjected to statistical evaluation with a level of significance at P < 0.05 and the results were formulated. Results: Concerning marginal bone loss, it was seen that for delayed loading, the bone loss at the implant level was 1.52 ± 0.14, 0.19 ± 0.11, and 0.40 ± 0.12, respectively, at placement, 1 and 2 years. Plaque and mucosal bleeding scores were low at the time of placement with respective values of 0.96 ± 0.12 and 28.42 ± 3.15 for the delayed loading group and 0.98 ± 0.11 and 30.24 ± 3.15 for the immediate loading group. Tartrate-resistant acid phosphatase (TRAP) showing remodeling was high at 3 months in delayed loading (13.3 ± 8.5). Alkaline Phosphatase (ALP) was highest in delayed loading at 3 months (25.2 ± 7.7) and immediate loading at 2 days (32.6 ± 13). Conclusion: Both immediate loading and delayed loading implants show similar results in terms of bone loss, soft-tissue parameters, and biomarkers in sulcular fluids with relatively few and manageable complications.