Portugal, a medium- to low-level endemic country (21·6 cases/100 000 population in 2012), has one of the highest European Union tuberculosis (TB) incidences. Although incidence is declining progressively, the country's heterogeneity in both regional endemics and their evolution suggests the importance of a better understanding of subnational epidemiology to customize TB control efforts. We aimed to update knowledge on municipality-years pulmonary TB incidence clustering, identify areas with different time trends, and show the potential of combining complementary clustering methods in control of infectious diseases. We used national surveillance municipality-level data (mainland Portugal, 2000–2010). Space–time clustering and spatial variation in temporal trends methods were applied. Space–time critical clusters identified (P < 0·001) were still the Lisbon and Oporto regions. The global incidence declined at a 5·81% mean annual percentage change, with high space–time heterogeneity and distinct time trend clusters (P < 0·001). Municipalities with incidences declining more rapidly belonged to critical areas. In particular, the Oporto trend cluster had a consistent −8·98% mean annual percentage change. Large space–time heterogeneities were identified, with critical incidences in the greater Lisbon and Oporto regions, but declining more rapidly in these regions. Oporto showed a consistent, steeper decrease and could represent a good example of local control strategy. Combining results from these approaches gives promise for prospects for infectious disease control and the design of more effective, focused interventions.