<p>Out of 420 samples, 35% tested positive for AMR pathogens, with Coagulase-Negative Staphylococci (16.7%), Klebsiella pneumoniae (12.9%), and Acinetobacter spp. (5.6%) being the most prevalent. Resistance rates for Gentamicin, Cotrimoxazole, and Ciprofloxacin were alarmingly high (98-100%), while Amikacin demonstrated low resistance (3.0-5.56%), indicating potential efficacy. Among the neonates admitted, 91.8% survived, and 8.2% succumbed. Risk factor analysis revealed that improper PPE usage (AOR 3.90, p &lt; 0.001), non-functional handwashing sinks (AOR 3.20, p &lt; 0.001), and inadequate disinfection practices (AOR 2.70, p &lt; 0.001) were strongly associated with microbial contamination. Environmental factors, including cockroach presence (AOR 1.80, p = 0.040) and high traffic flow (AOR 2.10, p = 0.005), were also significant contributors. The qualitative data analysis confirmed that improper PPE use, inadequate disinfection practices, pest control challenges, and non-functional handwashing sinks significantly contributed to microbial contamination risks in the NICU, aligning with the quantitative findings.</p>