Smoking worsens tuberculosis (TB) outcomes. Persons with TB who smoke can benefit from smoking cessation. We report findings of a multi-country qualitative process evaluation assessing barriers and facilitators to implementation of smoking cessation behaviour support in TB clinics in Bangladesh and Pakistan. We conducted semi-structured qualitative interviews at five case study clinics with 35 patients and 8 health workers over a period of 11 months (2017–2018) at different time points during the intervention implementation phase. Interviews were conducted by trained researchers in the native languages, audio-recorded, transcribed into English and analysed using a combined deductive–inductive approach guided by the Consolidated Framework for Implementation Research and Theoretical Domains Framework. All patients report willingness to quit smoking and recent quit attempts. Individuals’ main motivations to quit are their health and the need to financially provide for a family. Behavioural regulation such as avoiding exposure to cigarettes and social influences from friends, family and colleagues are main themes of the interviews. Most male patients do not feel shy admitting to smoking, for the sole female patient interviewee stigma was an issue. Health workers report structural characteristics such as high workload and limited time per patient as primary barriers to offering behavioural support. Self-efficacy to discuss tobacco use with women varies by health worker. Systemic barriers to implementation such as staff workload and socio-cultural barriers to cessation like gender relations, stigma or social influences should be dealt with creatively to optimize the behaviour support for sustainability and scale-up.