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Weeds can harm crop growth and yield by competing for light, water, and nutrients and can produce high global potential yield losses if not controlled. However, the effects of weed diversity have not been fully examined. Here, we have used long-term data (31 years) of a cereal legume rotation from a locality in central Spain to determine the importance of internal and external (weather and weed diversity) factors on crop yield. We used a novel methodology based on dynamic systems to explore how weed diversity and weather factors interact with crop yields. The dynamic model used here integrated internal and external factors with additive or non-linear variants. We showed that internal processes (self-regulation) are involved in wheat and legume yield temporal fluctuations. The self-regulation of crop production appears to be stronger in cereal (85%) than in legume (45%) systems, and therefore legumes seem to be more sensitive to external variations. The legume crop was not affected by weed diversity but was instead negatively influenced by average temperature for the growing season. In wheat, there was a negative, non-linear response of yield to the interaction between richness and minimum temperature for the growing season. An improved understanding of the influence of weed diversity on crop yield may help to anticipate the effects of climate change and guide management practices to maintain crop productivity under sustainable agriculture.