Improved understanding of the influence of climate on agricultural production is needed to cope with expected changes in temperature and precipitation, and an increasing number of undernourished people in food insecure regions. Many studies have shown the importance of seasonal climatic means in explaining crop yields. However, climate variability is expected to increase in some regions and have significant consequences on food production beyond the impacts of changes in climatic means. Here, we examined the relationship between seasonal climate and crop yields in Tanzania, focusing on maize, sorghum and rice. The impacts of both seasonal means and variability on yields were measured at the subnational scale using various statistical methods and climate data. The results indicate that both intra- and interseasonal changes in temperature and precipitation influence cereal yields in Tanzania. Seasonal temperature increases have the most important impact on yields. This study shows that in Tanzania, by 2050, projected seasonal temperature increases by 2 °C reduce average maize, sorghum, and rice yields by 13%, 8.8%, and 7.6% respectively. Potential changes in seasonal total precipitation as well as intra-seasonal temperature and precipitation variability may also impact crop yields by 2050, albeit to a lesser extent. A 20% increase in intra-seasonal precipitation variability reduces agricultural yields by 4.2%, 7.2%, and 7.6% respectively for maize, sorghum, and rice. Using our preferred model, we show that we underestimate the climatic impacts by 2050 on crop yields in Tanzania by 3.6%, 8.9%, and 28.6% for maize, sorghum and rice respectively if we focus only on climatic means and ignore climate variability. This study highlights that, in addition to shifts in growing season means, changes in intra-seasonal variability of weather may be important for future yields in Tanzania. Additionally, we argue for a need to invest in improving the climate records in these regions to enhance our understanding of these relationships.