Sperm preparation is a critical step in assisted reproduction, aiming to isolate spermatozoa with optimal characteristics and high fertilizing potential. Traditional sperm selection methods involve centrifugation, which may cause sperm damage. Microfluidic sperm sorting (MSS) offers an alternative approach, mimicking the female reproductive tract environment, avoiding centrifugation, and reducing manipulation and processing time. This study aims to compare the performance of MSS and Swim-up (SU) in 26 normozoospermic, 31 hyperviscous normozoospermic, 15 oligozoospermic, and 9 asthenozoospermic subjects. Semen samples were collected from male subjects undergoing routine semen analysis at Careggi University Hospital, Florence. Sperm selection was carried out using both SU and MSS. The parameters assessed included sperm motility, viability, concentration, kinematics, DNA fragmentation (sDF), chromatin compaction, and oxidative status. Both SU and MSS improved sperm characteristics compared to unselected samples. MSS isolated high-quality spermatozoa with lower sDF and higher chromatin compaction than SU, not only in normozoospermic samples but also in samples with semen defects like hyperviscosity, low concentration and/or motility, and high sDF. In conclusion, the use of microfluidics may enhance the chances of successful fertilization and improve reproductive outcomes, especially for individuals with compromised semen quality where conventional methods may fail.