Objectives: To determine the impact of rectal swabs (RSs) on infectious complications (IC) following prostate biopsy (PB). Methods: A retrospective cohort study was conducted including all patients subjected to PB between 2009 and 2013. Group B consisted of patients with a RS and group A of patients without. RS reported the presence of gram-positive or negative germs, sensitive or resistant to ciprofloxacin. Antimicrobial prophylaxis was adjusted to the result. Frequency of IC in each group was determined. Results: Group B had 548 (47.20%) patients and group A 613 (52.80%). From group B, 250 (45.62%) of the RSs showed fluoroquinolone (FQ)-resistant germs. Forty nine (16.44%) patients with sensitive germs vs. 147 (59.51%) with resistant germs had a history of previous FQ treatment (p < 0.0001). IC were observed in 33 (5.49%) patients from group A and in 7 (1.28%) patients from group B (p < 0.0001), requiring hospitalization in 4.99 vs. 1.28%, respectively. IC and hospital admissions were reduced in 76.68 and 74.34%, respectively, following the implementation of RS. Conclusions: RS and targeted antibiotic prophylaxis prior to PB was associated with a significant reduction in IC and hospital admissions. Ceftriaxone could be an alternative in cases of known resistance. Past history of FQ treatment is associated with increased resistance.