This study investigates the causes of pronounced low precipitation bias over Amazonia in the Community Atmosphere Model version 5 (CAM5), a common feature in many global climate models. Our analysis is based on a suite of 3-day long hindcasts starting every day at 00Z from 1997 to 2012 and an AMIP simulation for the same period. The Amazonia dry bias appears by the second day in the hindcasts and is very robust for all the seasons with the largest bias magnitude during the wet season (December–February). The bias pattern and magnitude do not change much during different dynamical wind regimes on sub-seasonal time scales. We further classify the diurnal cycle of precipitation near the LBA sites from observations and hindcasts into three convective regimes: no precipitation, late afternoon deep convection, and nighttime deep convection. CAM5 can only simulate the late afternoon convective regime and completely fails to simulate the nighttime convection, which is mostly from propagating convective systems originating from remote locations. CAM5 mainly underestimates precipitation in the late afternoon and nighttime convective regimes, which occur during ∼67% of wet season days and account for ∼75% of accumulated precipitation amount in observations. The persistent warm temperature bias and slightly higher moisture below 850 mb likely trigger deep convection too frequently, resulting in an earlier but weaker rainfall peak in the diurnal cycle. Furthermore, shallow convection may not effectively transport moisture from boundary layer to the free atmosphere, which also leads to weaker deep convection events.