Background: A key point in assessing dental implant prosthetic joints is their mechanical strength and biological response under the masticatory loading. The aim of the present systematic review was to evaluate the marginal bone loss and prosthetic behaviour of different internal/external bi-phasic implants. Methods: Randomized Clinical Trials (RCTs) have been considered for analytic purposes. The article screening was conducted on the Pubmed/MEDLINE, EMBASE and Google Scholars databases through an electronic process. Eligibility and risk of bias assessments were conducted for an article to be included in the data process. A series of pairwise meta-regressions for continuous variables was conducted considering the mean differences and 95% CI at two different timepoints: baseline and 1-year follow-up. The meta-analysis was performed comparing the following groups: internal conical prosthetic joint with index (IC), external hexagon bone level position (EI), internal tri-channel connection bone level position (ITC), internal hexagon 1 mm below the bone level (HI), internal hexagon bone level position (HI crest), cone morse 1 mm below the bone level (CM), cone morse bone level position (CM crest) and internal octagon bone level position (IO). The following parameters were considered for descriptive data synthesis: sample size, implant manufacturer, prosthetic joint type, prosthetic complications, marginal bone loss, study outcomes. Results: A total of 247 papers were identified by the electronic screening and 241 were submitted for the full text assessment. The eligibility process excluded 209 articles, and 32 studies with a low risk of bias were considered for the qualitative synthesis and further statistical methods. At the baseline, the CM showed a more effective efficiency and reduced marginal bone loss compared to IC, EI, ITC, internal hexagon, cone morse and internal octagon (p < 0.05). CM showed the lower rate of prosthetic complications and structural device failure including abutments and joint components under the loading compared to other joint types. Conclusion: Within the limits of the present investigation, the heterogeneity, the weight of the study model considered and the inherent differences between the dental implant properties, the pure CM showed a more consistent control of marginal bone loss at short- and medium-term follow-up. Despite the low rate of cumulative complications for all joints considered, the CM abutment joints were less prone to prosthetic failure at an early and medium-term follow-up.