As exemplified by the situation in Cambodia, disease specific (vertical) health programmes are often favoured when the health system is fragile. The potential of such an approach to impede strengthening of primary healthcare services has been studied from a health systems perspective in terms of access and quality of care. In this bottom-up, qualitative study we investigate patient and community member experiences of health services when a strong tuberculosis (TB) programme is embedded into a relatively underutilized primary healthcare system. We conducted six gender-stratified community focus group discussions (n = 49) and seven mixed-gender focus group discussions with TB patients (n = 45) in three provinces located in urban, peri-urban and rural areas of Cambodia. Our analysis of health-seeking behaviour and experiences for TB and TB-like illness indicates that building a strong vertical TB control programme has had numerous benefits, including awareness of typical symptoms and need to seek care early; confidence in free TB services at public facilities; and willingness to complete treatment. However, there was a clear dichotomy in experiences and behaviour with respect to care-seeking for less severe illness at primary health services, which were generally avoided owing to access barriers and perceived poor quality. The tendency to delay seeking health care until the development of severe symptoms clearly indicative of TB is a major barrier to early diagnosis and treatment of TB. Our study indicates that an imbalance in the strength of vertical and primary health services could be a lose-lose situation as this impedes improvements in health system functioning and constrains progress of vertical disease control programmes.