This study attempts to analyze the short- and long-run impacts of the probable change in rainfall and temperature simultaneously on food availability and access to food issues, as the two dimensions of food security, in Malaysia. It uses an integrated method comprising of a stochastic method and a computable general equilibrium model using the latest (2010) input–output table published in 2015. The stochastic method, which relates to the Monte Carlo simulation, provides the probable changes in rainfall and temperature patterns and their probability of occurrence based on historical data of rainfall and temperature and crop productivity. It was found that, simultaneous variation of rainfall and temperature, in both the short- and long-run, contracts the economic performance of Malaysia. Findings also show the negative impact of rainfall–temperature variability, in both time periods, on food availability and access to food due to a reduction in the supply of agricultural products, a commodity inflation pressure and a reduction in household income. Moreover, results suggest that the climate variability shocks lead to a reduction in the consumption and welfare of all household groups, particularly in rural areas.