Tail integrity is a key welfare target in European pig farming. This study evaluated the welfare condition of weaner (28–84 days old) pigs with docked (D) and undocked (UD) tails on a commercial farm, following National Reference Center for Animal Welfare and WelfareQuality® standards. Animal-Based Measures and the hormonal quantification of cortisol (CORT) and dehydroepiandrosterone sulfate (DHEA(S)) in bristle samples were assessed in 295 pigs distributed in 16 pens. Pigs were born from 24 homogenous sows, distributed across four consecutive weekly batches, and were balanced by sex. Compared with D pigs, UD pigs presented more injuries in the tail (P = 0.02) and on the body (P < 0.01), with tail biting occurrences peaking halfway through the post-weaning phase. Body injuries increased over time, particularly in UD pigs, correlating with rising stocking density. D pigs displayed a straight tail posture more frequently (P < 0.01), suggesting a more positive emotional state. Regardless of tail condition, the use of environmental enrichments declined over time (P = 0.03) as novelty diminished. Hormonal analysis revealed sex-related differences in resilience, with females showing higher CORT and CORT/DHEA(S) ratio and lower DHEA(S) levels than castrated males (P < 0.01). There was a tendency toward higher CORT/DHEA(S) ratio in UD pigs than D ones (P = 0.06), indicating a greater activation of the hypothalamic-pituitary-adrenal axis to restore homeostatic conditions. Multivariate analysis linked body lesions, stress markers, and negative interactions, highlighting welfare's multifactorial nature. Tail integrity alone may be misleading as a welfare indicator. A holistic assessment, integrating physical, emotional, and physiological factors, is crucial for improving management strategies for UD pigs on commercial farms.