The aim of this study was to determine the effects of loading density and gender on blood welfare indicators, carcass bruises and horsemeat quality. Data were collected from twelve transports of 89 slaughter horses originating from the same collection centre. The transportation of slaughter horses at high loading densities (>200 kg/m2), especially stallions, resulted in increased levels of lactate (p = 0.021), glucose (p < 0.0001), ceruloplasmin (p < 0.0001) and AOPP (p < 0.0001), but lower GSH levels (p < 0.0001). Compared to stallions and mares, geldings subjected to high loading density (>200 kg/m2) during transport had lower levels of the aforementioned blood metabolites. In addition, stallions exposed to a high load density (>200 kg/m2) had the highest frequency of severe (p = 0.0002), large (p < 0.0001) and circular (p = 0.0001) carcass bruises, which were predominantly located on the abdominal (p = 0.0056) and thoracic (p = 0.0004) wall. In contrast, a higher percentage (p < 0.0001) of undamaged carcasses was found in slaughter horses exposed to a low loading density (≤200 kg/m2) during transport. Stallions exposed to high loading densities (>200 kg/m2) during transport had the highest initial pH (p < 0.0001) and ultimate pH (p = 0.005) in terms of m. longissimus lumborum and redness (p = 0.017), but the lowest drip loss (p = 0.050) and lightness (p < 0.0001), which, consequently, led to the highest (p = 0.0045) proportion of DFD-like defects in the meat quality. In conclusion, the results of this study showed that high loading densities (>200 kg/m2), regardless of gender, negatively affect horse welfare during transport. In addition, stallions were more sensitive to poor pre-slaughter conditions and produced the lowest meat quality, while geldings were the most resistant. To determine the optimal transport density, further research is needed to determine the effects of different loading densities on the behaviour, physiology, carcass and meat quality of slaughter horses.