A recovery plan was developed for the threatened spiny softshell turtle (Apalone spinifera) population in the province of Quebec, which included the implementation of a head-start program with the objective of increasing juvenile survival over the first winter. High mortality rates were observed during the first two years of the program (2014: 22.5% [7/31], 2015: 55.0% [22/40]). Mortalities for both years were associated with an unusually high occurrence of coelomitis consecutive to a confirmed (N = 11) or suspected (N = 4) gastro-duodenal perforation. Microscopically, the coelomitis consisted of serosal mesothesial cell hypertrophy, fibrinous to granulomatous inflammation, visceral adhesions, as well as the presence of bacterial colonies and alimentary particles. Marked dilation of the gastrointestinal tract associated with abundant food material, suggestive of a digestive impaction/ileus, was frequently observed with the coelomitis cases. During the second year of the program, the increase in the quantity of food offered and the substitution of freeze-dried Gammarus shrimp with larger and more abrasive sun-dried red shrimps (Solenocera melantho) were identified as potential risk factors for gastrointestinal perforations and could account for the increased mortality rate observed. Prospective dietary studies are warranted to establish optimal diet parameters in juvenile individuals from this species.