Perennial crops are among the most valuable of California’s diverse agricultural products. They are also potentially the most influenced by information on future climate, since individual plants are commonly grown for more than 30 years. This study evaluated the impacts of future climate changes on the 20 most valuable perennial crops in California, using a combination of statistical crop models and downscaled climate model projections. County records on crop harvests and weather from 1980 to 2005 were used to evaluate the influence of weather on yields, with a series of cross-validation and sensitivity tests used to evaluate the robustness of perceived effects. In the end, only four models appear to have a clear weather response based on historical data, with another four presenting significant but less robust relationships. Projecting impacts of climate trends to 2050 using historical relationships reveals that cherries are the only crop unambiguously threatened by warming, with no crops clearly benefiting from warming. Another robust result is that almond yields will be harmed by winter warming, although this effect may be counteracted by beneficial warming in spring and summer. Overall, the study has advanced understanding of climate impacts on California agriculture and has highlighted the importance of measuring and tracking uncertainties due to the difficulty of uncovering crop-climate relationships.