The purpose of ante- and post-mortem inspections at slaughterhouses is to ensure that meat and other relevant food products of animal origin are safe for human consumption. However, these inspections can also be useful for detecting animal health and welfare issues. In cattle, traumatic injuries from on-farm incidents, transport or handling at the slaughterhouse are indications of both reduced animal welfare and increased risk of food waste, ultimately resulting in economic losses for both farmers and slaughterhouses. This observational study aimed to investigate the prevalence and seasonal variation of traumatic injuries in cows and heifers reared on organic and conventional farms in Sweden. The study includes slaughter remarks and condemnations from meat inspection data from 336,071 animals slaughtered between 2020 and 2022. Two types of injuries were analysed: “chronic traumatic injuries” (CTI) sustained on-farm and “acute traumatic injuries” (ATI) sustained during transport or at the slaughterhouse. Logistic regression models were developed to assess the influence of production system and season. Results show a higher prevalence of CTI in animals from conventional farms (9.8%) compared to organic farms (6.9%; P < 0.001), which may indicate that animals from organic farms are managed and handled in a way that makes them better prepared for challenges that they are later exposed to on-farm prior to slaughter. ATI were more frequent in animals from organic farms during the grazing period (interaction between production system and season: P = 0.002), which may indicate that animals from organic farms find the transition to the slaughterhouse environment more abrupt and stressful during the grazing period. Condemnations due to injuries were significantly higher for animals with CTI or ATI compared to animals without these specific remarks. These findings highlight the importance of pre-slaughter management, both on-farm and at the slaughterhouse, and slaughterhouse design in improving animal welfare and reducing food as well as economic losses associated with carcase condemnations.