Convection-permitting modeling allows us to understand mechanisms that influence rainfall in specific regions. However, microphysics parameterization (MP) and planetary boundary layer (PBL) schemes remain an important source of uncertainty, affecting rainfall intensity, occurrence, duration, and propagation. Here, we study the sensitivity of rainfall to three MP [Weather Research and Forecasting (WRF) Single-Moment 6-class (WSM6), Thompson, and Morrison] and two PBL [the Yonsei University (YSU) and Mellor–Yamada Nakanishi Niino (MYNN)] schemes with a convection-permitting resolution (4 km) over northwestern South America (NWSA). Simulations were performed by using the WRF model and the results were evaluated against soundings, rain gauges, and satellite data, considering the spatio-temporal variability of rainfall over diverse regions prone to deep convection in NWSA. MP and PBL schemes largely influenced simulated rainfall, with better results for the less computationally expensive WSM6 MP and YSU PBL schemes. Regarding rain gauges and satellite estimates, simulations with Morrison MP overestimated rainfall, especially westward of the Andes, whereas the MYNN PBL underestimated precipitation in the Amazon–Savannas flatlands. We found that the uncertainty in the rainfall representation is highly dependent on the region, with a higher influence of MP in the Colombian Pacific and PBL in the Amazon–Savannas flatlands. When analyzing rainfall-related processes, the selection of both MP and PBL parameterizations exerted a large influence on the simulated lower tropospheric moisture flux and moisture convergence. PBL schemes significantly influenced the downward shortwave radiation, with MYNN simulating a greater amount of low clouds, which decreased the radiation income. Furthermore, latent heat fluxes were greater for YSU, favoring moist convection and rainfall. MP schemes had a marked impact on vertical velocity. Specifically, Morrison MP showed stronger convection and higher precipitation rates, which is associated with a greater latent heat release due to solid-phase hydrometeor formation. This study provides insights into assessing physical parameterizations in numerical models and suggests key processes for rainfall representation in NWSA.