Background: Multiparametric Magnetic Resonance Imaging (mpMRI)-based targeted biopsy has shown to be beneficial in detecting Clinically Significant Prostate Cancer (csPCa) and avoiding diagnosis of Non-csPCa (ncsPCa); however, its role in the treatment of biopsy-naïve patients is still under discussion. Methods: After identifying predictors for the diagnosis of csPCa via Multivariate Logistic Regression Analysis (MLRA), a propensity-score (1:1 nearest neighbor) matched comparison was performed between a Systematic-Only Biopsy (SOB) cohort and a mpMRI-based Combined (systematic + targeted) Biopsy (CB) cohort from two tertiary urologic centers (SOB: Department of Urology, University General Hospital of Heraklion, University of Crete, School of Medicine, Heraklion, Crete, Greece; CB: LKH Hall in Tirol, Austria). Only biopsy-naïve patients were included in the study. The study period for the included patients was from February 2018 to July 2023 for the SOB group and from July 2017 to June 2023 for the CB group. The primary outcome was the diagnosis of csPCa (≥ISUP 2); secondary outcomes were overall cancer detection, the added value of targeted biopsy in csPCa detection, and the reduction in ncsPCa diagnosis with CB compared to SOB. To estimate the Average Treatment effect of the Treated groups (ATT), cluster-robust standard errors were used to perform g-computation in the matched sample. p-values < 0.05 with a two-sided 95% confidence interval were considered statistically significant. Results: Matching achieved well-balanced groups (each n = 140 for CB and SOB). In the CB group, 65/140 (46.4%) patients were diagnosed with csPCa compared to 44/140 (31.4%) in the SOB group (RR 1.48, 95%-CI: 1.09–2.0, p = 0.01). In the CB group, 4.3% (6/140) and 1.4% (2/140) of csPCa cases were detected with targeted-only and systematic-only biopsy cores, respectively. In the CB group, 22/140 (15.7%) patients were diagnosed with ncsPCa compared to 33/140 (23.6%) in the SOB group (RR = 0.67, 95% CI: 0.41–1.08, p = 0.1). When comparing SOB to CB (ATT), the marginal OR was 0.56 (95% CI: 0.38–0.82, p = 0.003) for the diagnosis of csPCa and 0.75 (95% CI: 0.47–1.05, p = 0.085) for the diagnosis of overall cancer (≥ISUP 1). Conclusion: The CB approach was superior to the SOB approach in detecting csPCa, while no additional detection of ncsPCa was seen. Our results support the application of mpMRI for biopsy-naïve patients with suspicions of prostate cancer.