East Africa is wetter in CMIP5 historical runs than AMIP runs during the OND short rains season, but drier in the MAM long rains season.

The AMIP run of MRI-CGCM3 reproduces the observed rainfall annual cycle over East Africa very well while its coupled historical run has a similar but stronger bias as the coupled multimodel mean. Therefore, MRI-CGCM3 serves as an exemplary model to study the coupled model induced rainfall bias over East Africa.

The historical\(-\)AMIP monthly climatology rainfall bias can be explained by the bias in CI, which, itself is dominated by the bias in near surface MSE. The moisture component is the dominant term in the near surface MSE while the temperature component is secondary.

The near surface MSE bias of historical\(-\)AMIP is modulated by SST bias over the western Indian Ocean.

Insufficient ocean dynamical cooling and latent flux both are responsible for the development of the warm SST bias of historical\(-\)AMIP in MRI-CGCM3, while insufficient short wave radiation and excess latent heat flux mainly contribute to the cold SST bias.