Objective The aim of the study was to analyze bacterial flora in venous leg ulcers, empiric and targeted antibiotic therapy, and factors influencing healing time. Materials and methods Data from 30 patients with venous leg ulcers were retrospectively analyzed. Collected data included: sociodemographic data, wounds information, number of comorbidities, results of the microbiological examination, and empiric and targeted antibiotic therapy. To compare the empiric and targeted treatment in terms of their compatibility, the group of patients was divided into the four subgroups: NEA (no empiric antibiotics), NA (no antibiotics), ETA+ (compatibility of empiric and targeted antibiotic), ETA− (no compatibility of empiric and targeted antibiotic). Results The average ulcer healing time was 163.4 ± 97.1 (range 51.0 to 426.0) days and increased by 28 days with each additional bacterial strain in the ulcer (p = 0.041). Healing time did not differ between the four groups. Staphylococcus aureus and Pseudomonas aeruginosa were the most frequent bacteria. Amoxicillinium/acidum clavulanicum was the most common empirical antibiotic and amoxicillinium/acidum clavulanicum, and levofloxacinum was the most common targeted antibiotic. Conclusions Venous leg ulcer healing time was prolonged with each subsequent bacterial strain in the ulcer, and it was independent from systemic antibiotic therapy.