Bovine tuberculosis (bTB) is a chronic granulomatous disease that primarily affects lung tissue and lymph nodes (LN) in cattle, with economic impact on their productivity. Furthermore, it is potential zoonoses that may cause public health hazard. In this study, we evaluated the presence of bTB in two abattoirs: Cayambe and Pelileo countries located in the Ecuadorian provinces of Pichincha and Tungurahua, respectively. In total, 578 cattle were sampled (Cayambe 271 and Pelileo 307): 1,156 LN and 578 lung tissue samples were collected to apply in vitro culture and nested-PCR, respectively. The results determined a total apparent prevalence of 4.33%, with 4.06% at Cayambe's abattoir and 4.56% at Pelileo's abattoir. Additionally, the Bayesian analysis showed a total true prevalence of 2.51%, with 89.7% of sensitivity and 97.6% of specificity. The risk factors were evaluated by the use of simple logistic regressions with and without the random effect of places of origin. Associations of the origin of cattle in the selected slaughterhouses were found. The results showed an efficient method for the detection of bTB, which could identify a large number of infected animals, and the usefulness of lung tissue samples for early diagnosis of the disease was demonstrated in this study.