This study aims to evaluate, via a mixed methods study, the implementation of the screening process for pulmonary tuberculosis (PTB) within indigenous population of the Department of Cauca, Colombia, during the 2016-2018 period. Indicators assessing the PTB screening process were elaborated and estimated. Subsequently, an evaluation of the indicators were performed based on a sampling process from health care providers of the municipalities with the highest and lowest PTB incidence and from key agents' perspective. Screening indicators were estimated and thematic analysis was performed based on the interviews conducted with key agents. Finally, a triangulation of quantitative and qualitative findings was performed. From the total population expected to have respiratory symptomatics (n = 16,711), the health care providers were able to identify 42.3% of them. Out of the individuals identified as respiratory symptomatics (n = 7,064), they were able to examine 93.2% (n = 6,585) with at least one acid-fast bacilli smear test. The reported positivity index from acid-fast bacilli smear test was 1.87%. The explanations from key agents revolved around the possibility of an overestimated targeted amount of respiratory symptomatics; insufficient personnel for the search of symptomatic individuals; high costs for the search in areas of difficult access; the need to request permissions from indigenous authorities; culturally ingrained stigma; use of traditional medicine and self-medication; and patient's personal beliefs. This study revealed barriers in the implementation of the screening process for PTB within the indigenous population from the Department of Cauca, mainly in the identifying process of the respiratory symptomatics.