Cronobacter sakazakii is a Gram-negative bacterium known for causing severe infections in neonates, particularly through contaminated infant formula. This study investigated the role of the outer membrane lipoprotein NlpD in the environmental tolerance of C. sakazakii. A nlpD knockout mutant was constructed, and its impact on desiccation resistance, biofilm formation, motility, and proteomic profiles was evaluated and compared with that of the wild-type strain. The nlpD mutant presented reduced desiccation tolerance, reduced ability to form a biofilm, and altered surface hydrophobicity and motility patterns. The complemented strain restored these phenotypic changes, confirming that the observed effects were specifically due to the deletion of nlpD. Proteomic analysis revealed significant differential expression of proteins involved in metabolic and biosynthetic pathways upon nlpD deletion. These findings emphasize the multifaceted role of NlpD in enhancing the environmental tolerance of C. sakazakii, suggesting its importance in the resilience and survival of the bacterium in adverse conditions.