Changes in climate patterns are the main challenges being faced by the coffee and cocoa production systems, one of the key sources of livelihood for farmers in Togo’s humid dense forests zone, also known as “Togo ecological zone IV”. The objective of this study was to analyze the climatic vulnerability of coffee-cocoa agroforestry systems (CCAFS) in Togo ecological zone IV both ongoing (last 40 years 1980–2019) and the incoming decades (by 2050) considering climate forecast under AR6 socioeconomic pathways. The Standardized Precipitation Index (SPI) approach with the Mann–Kendall & Sen’s tests and the MaxEnt tool were used to assess the drought condition and the potential impacts on CCAFS suitability in the study area. The results show instability in rainfall series with a non-significant progressive trend in the area during the past four decades, while a significant increase in temperature was observed. Beyond 2050, suitable areas for coffee and cocoa species will drift to the pic mountainous part. Thus, respectively 51.91 and 54.50% of currently suitable areas for the two species, will be lost under the future climate scenario SSP3-7.0 and SSP5-8.5. These losses are mainly due to the reduction of precipitation of the driest month (Bio14), precipitation of the driest quarter (Bio17), and precipitation of the coldest quarter (Bio19) of the year. Drought is therefore revealed as the main limiting climatic factor for coffee and cocoa in Togo. The increasing drought intensity in the future is a source of high vulnerability of CCAFS as well as the local farmers’ livelihoods.