Purpose To compare the block sequential regularized expectation maximization (BSREM) algorithm with the ordered subsets expectation maximization (OSEM) algorithm and to evaluate how different penalty factors (bvalues) influence image quality and SUV measurements. Methods We analyzed data from 78 prostate cancer patients who underwent(68)Ga-RM2 (n = 42) or(68)Ga-prostate-specific membrane antigen (PSMA)-11 (n = 36) PET/MRI. The raw PET data were retrospectively reconstructed using both time-of-flight (TOF)-BSREM withbvalues of 250, 350, 500, 750, and 1000 and TOF-OSEM. Each reconstruction was reviewed independently by 3 nuclear medicine physicians and scored qualitatively using a Likert scale (1 = poor, 5 = excellent quality). SUV measurements were analyzed as well. Results Fifty-seven lesions were detected (21 on(68)Ga-RM2 and 36 on(68)Ga-PSMA-11 PET/MRI); SUVmax decreased with the increase of beta values for both tracers. Background noise (SUVsd) decreased with increasing of beta values for both tracers. The mean +/- SD scores for(68)Ga-RM2 PET images were 2.4 +/- 0.5 forb= 250 reconstructions, 3.2 +/- 0.6 forb= 350, 4 +/- 0.6 forb= 500, 4.5 +/- 0.5 forb= 750, 4.4 +/- 0.7 forb= 1000, and 3.4 +/- 0.6 for TOF-OSEM. The mean +/- SD scores for(68)Ga-PSMA-11 PET images were 3.2 +/- 0.8 forb= 250 reconstructions, 4.1 +/- 0.8 forb= 350, 4.7 +/- 0.6 forb= 500, 4.8 +/- 0.4 forb= 750, 4.7 +/- 0.6 forb= 1000, and 3.8 +/- 0.5 for TOF-OSEM. Conclusions Time-of-flight-BSREM algorithm improves image quality. Differentbvalues should be used for different(68)Ga-labeled radiopharmaceuticals such as those targeting GRPR and PSMA receptors. Once selected, the samebvalue should be consistently used because SUVmax measurements differ with differentbvalues.