Although incorporating proteases into sperm medium is considered the most effective procedure to eliminate camel semen viscosity, it drastically affects viability, morpho‐functional properties and, hence, fertilization potential of spermatozoa. The present work aimed at evaluating adequacy of employing magnetic nanoparticles‐based sperm purification technique for eluting impaired and apoptotic camel spermatozoa from cryopreserved semen doses following protease‐based semen liquefaction. Thirty cryopreserved semen doses (50 x 106 sperm/straw) representing the following liquefaction treatments: control (untreated), 0.1 mg/ml papain or 5 U/ml bromelain were used (n = 10 straws per treatment). Immediately after thawing (38°C for 40 s), sperm concentration of each straw within treatment was readjusted to 15 x 106 sperm/mL by dilution in PBS (37°C). Sperm physical and cytological properties were then assessed (non‐purified semen). Thereafter, each specimen was subjected to lectin‐functionalized DNA‐defrag magnetic nanoparticles sperm purification, and the same sperm traits were re‐evaluated after undergoing purification (purified semen). Sperm DNA fragmentation level within each group, prior to and after magnetic nano‐purification, was also determined by fluorescent imaging. The results showed a dramatic improvement (p < .05) in post‐thaw motility (%), viability (%), normal sperm (%), intact acrosome (%) and HOST‐reacted (%) spermatozoa in protease‐liquefied semen following sperm magnetic nano‐purification. Additionally, the highest (p < .05) DNA fragmentation level was recorded in all cryopreserved semen groups prior to purification, whereas the lowest (p < .05) was observed in the protease‐treated specimens after magnetic nano‐purification. These results indicate that protease‐based semen liquefaction prior to cryopreservation in conjunction with magnetic nano‐purification post‐thawing holds potential for reducing the proportion of damaged and dead spermatozoa, hence improving camel sperm fertilization competence.