To explore the potential impacts of climate change on precipitation and mesoscale convective systems (MCSs) in the Peruvian Central Andes, a region with complex terrain, two future and one historical convection-permitting regional climate simulations are conducted using the Weather Research and Forecasting (WRF) model. All simulations adopt consistent model configurations and two nested domains with grid spacings of 15 and 3 km covering the entire South America and the Peruvian Central Andes, respectively. The future simulations are run for 2070-2080 and driven by a bias-corrected global dataset derived from the Coupled Model Intercomparison Project Phase 6 (CMIP6) ensemble under the SSP2-4.5 and SSP5-8.5 emission scenarios. Results show geographically dependent changes in annual precipitation, with a consistent rise in the frequency of intense hourly precipitation across all examined regions. The western Amazon Basin shows a decrease in annual precipitation, while increases exist in parts of the Peruvian west coast and the east slope of the Andes under both future scenarios. In the warming scenarios, there is an overall increase in the frequency, precipitation intensity, and size of MCSs east of the Andes, with MCS precipitation volume increasing by up to ~22.2%. Despite consistently enhanced synoptic-scale low-level jets in future scenarios, changes in low-level dynamic convergence are inhomogeneous and predominantly influence annual precipitation changes. The increased convective available potential energy (CAPE), convective inhibition (CIN), and precipitable water (PW) in a warming climate suppress weak convection, while fostering a more unstable and moisture-rich atmosphere facilitating more intense convection and the formation and intensification of heavy precipitation-producing MCSs. The study highlights the value of convection-permitting climate simulations in projecting future severe weather hazards and informing climate adaptation strategies, especially in regions characterized by complex terrain.