Background: Dental caries in children often require crowns for restoration, with options like stainless steel, zirconia and Bioflex enhance accuracy, efficiency, and patient satisfaction, offering a modern alternative to traditional methods. Objectives: The current trial aimed to determine the clinical outcomes, gingival health, and microbiological impacts of Bioflex crowns in comparison with prefabricated zirconia crowns (ZRCs) on Pulpotomized primary molars. Patients and methods: This study was conceived as a randomized controlled clinical trial. A total of 48 Pulpotomized mandibular second primary molars from 48 children were randomly allocated into two equal groups. 24 molars were re-established with prefabricated primary ZRCs (Control group), and an equal number were re-established with Bioflex crowns (study group). The Modified California Dental Association (CDA) protocol was applied to assess clinical performance, while gingival status was evaluated using the gingival and plaque indices. The bacterial effects were determined through microbial analysis. Results: Both types of restorations demonstrated comparable gingival health status throughout the follow-up period. For Marginal integrity and morphology both groups showed comparable results with non-significant differences at the follow-ups. Surface characteristics for Zirconia and Bioflex crown at the ends of follow up was 100%, 81.8% respectively (P=0.030). For bacterial adhesion Zirconia crown shows sustained anti-microbial effects over Bio-flex crown. Conclusions: The clinical performance and gingival health outcomes of Bioflex crowns were comparable to those of ZRCs, except for surface characteristics, which favored the ZRCs. However, Streptococcus mutans and Lactobacillus adhesion was significantly elevated on Bioflex crowns than on ZRCs.