This paper investigates the process behind climate model biases, especially in rainfall, during the southwest (June to August; JJA) and northeast monsoon (December to February; DJF) seasons over the Philippines using the downscaled Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations of the Southeast Asia Regional Climate Downscaling/Coordinated Regional Climate Downscaling Experiment-Southeast Asia (SEACLID/CORDEX-SEA). Biases in the surface and near-surface climate are assessed over land in eastern (EastPH) and western (WestPH) Philippines using observation and reanalysis datasets. Results show that models with well-represented sea surface temperature (SST) provided better added values after downscaling. Although the CMIP5-driven models tend to overestimate both surface energy and water partitioning, simulations with well-represented SST have better surface energy partitions. In contrast to the reference simulation driven by ERA-Interim reanalysis, the CMIP5-driven simulations tend to underestimate (overestimate) moisture flux convergence during the DJF (JJA) season, which might have contributed to the overall underestimation (overestimation) of rainfall in this season. Further investigation along a vertical transect shows the differences in governing mechanisms for each season. During DJF (JJA) season, the simulation with underestimated (overestimated) SST, near-surface air temperature, and mixing ratio results in underestimated (overestimated) rainfall over EastPH (WestPH). In addition, the CMIP5-driven models were found to overestimate low-level winds, which may have induced the deep convection regardless of season, suggesting the role of low-level winds in the convection scheme used in RegCM4 aside from topography and land cover.