<p>European Union regulations stipulate that only clean animals can be delivered for slaughter. In Germany, this is specified by a scheme in the national administrative regulation, categorizing delivery batches into “clean” or “not clean”. This study investigated whether the visual cleanliness of pigs upon arrival at the abattoir affects the microbial status [measured by total viable count (TVC) and Salmonella] at two points in the slaughter process line: in the lairage and after singeing/flaming. Additionally, the impact of the husbandry system (conventional/organic) on visual cleanliness and microbial status was examined. During unloading, 20 pig delivery batches were visually assessed. TVC and Salmonella were examined in the lairage and after singeing/flaming. Even pigs with high initial visual and microbial contamination showed TVC levels comparable to cleaner pigs after singeing/flaming. Comparing mean TVCs between husbandry systems, no significant differences were observed. Salmonella was detected only on pig skin sampled in the lairage (3%, 4/120). The study shows that effective process hygiene at the abattoir, particularly up to singeing/flaming, can reduce the bacterial load regardless of pigs’ initial cleanliness.</p>