BACKGROUND: Strengthening primary care is considered a global strategy to address non-communicable diseases and their comorbidity. However, empirical evidence of the longer-term benefits of capacity building programmes for primary care teams contextualised for low- and middle-income countries is scanty. In Thailand, a series of system-based capacity building programmes for primary care teams have been implemented for a decade. An analysis of the relationship between these systems-based trainings in diverse settings of primary care and quantified patient outcomes was needed. METHODS: Facility-based and community-based cross-sectional surveys were used to obtain data on exposure of primary care team members to 11 existing training programmes in Thailand, and health profiles and health-related quality of life of their patients measured in EuroQol-5 Dimension (EQ-5D) scale. Using a multilevel modelling, the associations between primary care provider's training and patient's EQ-5D score were estimated by a generalized linear mixed model (GLMM). RESULTS: While exposure to training programmes varied among primary care teams nationwide, District Health Management Learning (DHML) and Contracting Unit of Primary Care (CUP) Leadership Training Programmes, which put more emphasis on bundling of competencies and contextualising of applying such competencies, were positively associated with better health-related quality of life of their multimorbid patients. CONCLUSIONS: Our report provides systematic feedback to a decade-long investment on system-based capacity building for primary care teams in Thailand, and can be considered as new evidence on the value of human resource development in primary care systems in low- and middle-income countries. Building multiple competencies helps members of primary care teams collaboratively manage district health systems and address complex health problems in different local contexts. Coupling contextualised training with ongoing programme implementation could be a key entity to the sustainable development of primary care teams in low and middle income countries which can then be a leverage for improving patients outcomes.