Annual mass migrations of seabirds between their breeding and wintering grounds are critical for ensuring their survival and reproductive success. It is essential to comprehend their physical condition in order to identify the causes of death and to facilitate conservation efforts. This study focuses on evaluating the age, body condition index, and metabolites in liver and muscle (triglycerides, glycerol, glycogen, cholesterol, lactate, and glucose) of stranded Razorbills (n = 84) and Atlantic puffins (n = 11). The study was conducted along the Andalusian coast of Spain during the winter season of 2022–2023. The study examined the body condition of stranded individuals and their metabolic state to determine potential factors that may have caused their deaths. The study found that the majority of stranded individuals were juveniles. Both species exhibited low levels of carbohydrate (glucose and glycogen) in their tissues and high levels of lactate in their muscles. These findings could suggest that the individuals had undergone prolonged, strenuous exercise, demanding energy on anaerobic pathways, which may have been associated with migration. The study highlights the significance of adhering to standardized protocols when assessing the body condition of stranded seabirds. Doing so can help to identify causes of death and facilitate conservation efforts. A proposed index for body condition, which incorporates biometric measurements and individual physical condition, provides a comprehensive means of understanding the health of these unique species. This study underscores the importance of further research into the conservation measures and recommendations for protecting seabird populations. It is critical to comprehend the contributing factors of mass mortality incidents to work towards safeguarding these species and preserving their vital migration patterns.