Wild boar (Sus scrofa) and red deer (Cervus elaphus) are the main maintenance hosts for bovine tuberculosis (bTB) in continental Europe. Understanding Mycobacterium tuberculosis complex (MTC) excretion routes is crucial to define strategies to control bTB in free‑ranging populations, nevertheless available information is scarce. Aiming at filling this gap, four different MTC excretion routes (oronasal, bronchial‑alveolar, fecal and urinary) were investigated by molecular methods in naturally infected hunter‑harvested wild boar and red deer. In addition MTC concentrations were estimated by the Most Probable Number method. MTC DNA was amplified in all types of excretion routes. MTC DNA was amplified in at least one excretion route from 83.0% (CI 95 70.8–90.8) of wild ungulates with bTB‑like lesions. Oronasal or bronchial‑alveolar shedding were detected with higher frequency than fecal shedding (p < 0.001). The majority of shedders yielded MTC concentrations <10 3 CFU/g or mL. However, from those ungulates from which oronasal, bronchial‑alveolar and fecal samples were available, 28.2% of wild boar (CI 95 16.6–43.8) and 35.7% of red deer (CI 95 16.3–61.2) yielded MTC concentrations >10 3 CFU/g or mL (referred here as super‑shedders). Red deer have a significantly higher risk of being super‑shedders compared to wild boar (OR = 11.8, CI 95 2.3–60.2). The existence of super‑shedders among the naturally infected population of wild boar and red deer is thus reported here for the first time and MTC DNA concentrations greater than the minimum infective doses were estimated in excretion samples from both species.