The seismic design of buildings and infrastructure components requires the estimation of the hazard considering the dynamic response of the soil deposits, which substantially modifies the characteristics of the input motion at the rock basement. Seismic microzonation studies attempt to identify geologic zones of an area of interest with similar seismic hazard at a local scale. This paper presents a methodology to obtain seismic spectral amplification factors within each soil zone characterization considering the main sources of uncertainty. Results are presented in terms of spectral amplification factors for various seismic intensities and soil profile vibration periods. Design soil amplification factors can then be mapped using the measured vibration period of the soil profile at each location and the seismic intensity at bedrock for a given design return period. Response and design spectra may then be estimated at surface level for every location. Results can be easily integrated into probabilistic risk assessment platforms such as CAPRA (www.ecapra.org) for hazard and risk evaluations.