This cross-sectional survey evaluated hygiene and management practices of 160 small dairy farms in the Albaraka complex, Port Sudan, between November 2023 and December 2025. The study aimed to assess the relationship between herd management and bacterial quality of raw milk. A structured checklist examined four categories: cow and milk hygiene, housing and facilities, feed and water management, and biosecurity. Each item was scored on a 0–100% scale, with <70% rated poor, 70–79% good, 80–89% very good, and ≥90% excellent. The mean scores for each category were calculated to provide an overall evaluation of farm performance. Laboratory analyses of 80 milk and 10 water samples were conducted to determine Standard Plate Count (SPC) and Total Coliform Count (TCC). Results showed all categories were rated “Poor.” SPC in milk was uncountable, while mean TCC in milk was 430.63 cfu/ml ±450.19 and in water 700.00 cfu/ml ±235.70, far exceeding the acceptable limit of <100 cfu/ml. Correlation analysis revealed housing and facilities were positively associated with feed and water (r = 0.256; P<0.05), while cow hygiene, housing, and feed management strongly correlated with overall farm evaluation (P<0.001). TCC in milk was negatively correlated with biosecurity (r = -0.278; P<0.05). It could be concluded that the results revealed poor farm performance and alarming contamination levels of milk. Improved hygiene, sanitation, cooling, livestock health, and regulatory compliance are essential for safe milk production.