To assess the peri-implant soft tissue profiles between argon plasma treatment (PT) and non-treated (NPT) healing abutments by comparing clinical and histological parameters 2 months following abutment placement. Thirty participants were randomly assigned to argon-plasma treatment abutments group (PT) or non-treated abutments (NPT) group. Two months after healing abutment placement, soft peri-implant tissues and abutment were harvested, and histological and clinical parameters including plaque index, bleeding on probing, and keratinized mucosa diameter (KM) were assessed. Specialized stainings (hematoxylin–eosin and picrocirious red) coupled with immunohistochemistry (vimentin, collagen, and CK10) were performed to assess soft tissue inflammation and healing, and the collagen content keratinization. In addition to standard statistical methods, machine learning algorithms were applied for advanced soft tissue profiling between the test and control groups. PT group showed lower plaque accumulation and inflammation grade (6.71% vs. 13.25%, respectively; p-value 0.02), and more advanced connective tissue healing and integration compared to NPT (31.77% vs. 23.3%, respectively; p = 0.009). In the control group, more expressed keratinization was found compared to the PT group, showing significantly higher CK10 (>47.5%). No differences in KM were found between the groups. PT seems to be a promising protocol for guided peri-implant soft tissue morphogenesis reducing plaque accumulation and inflammation, and stimulating collagen and soft tissue but without effects on epithelial tissues and keratinization.