Objective: To compare the diagnostic performance of the 2 most common approaches of magnetic resonance imaging targeted biopsy (TB)—cognitive registration targeted biopsy (COG-TB) and software fusion targeted biopsy (FUS-TB)—we assessed our institutional experience with both methods. TB has emerged to complement systematic template biopsy (SB) in prostate cancer (PCa) diagnosis; however, which magnetic resonance imaging targeting methodology is diagnostically better remains unclear. Materials and methods: A total of 510 patients underwent TB at our institution before and after the adoption of fusion software with the UroNav platform (Invivo Corporation, Gainsville, FL). All patients had concurrent 12-core SB. We compared rates of clinically significant PCa detection, and rates of upstaging and missed diagnosis in reference to SB among patients who received COG-TB and patients who received FUS-TB. We also compared both COG-TB and FUS-TB results to their paired SB results. Results: The rates of upstaging or missing clinically significant PCa with FUS-TB (in reference to SB) was not significantly different from COG-TB (P = 0.172), nor was the risk of missing clinically significant PCa different between FUS-TB vs COG-TB on logistic regression (Odds ratio = 0.55, P = 0.106). No significant difference in biopsy outcomes was observed between FUS-TB and COG-TB (P = 0.171). We did find significant differences between FUS-TB and SB and between COG-TB and SB, with SB finding more clinically insignificant PCa (P < 0.001 and P = 0.04). Conclusion: In our institutional experience, no significant difference was observed between the diagnostic ability of COG-TB vs FUS-TB for detecting clinically significant PCa. Greater evidence demonstrating an advantage of FUS-TB over COG-TB would be required for clear recommendations in favor of FUS-TB.