<p>Organic agriculture can be an effective strategy to mitigate the negative effects of agriculture on people and the environment. Recent domestic and international initiatives have therefore sought to support the expansion of organic production while preserving environmental values integral to the movement. Based on the results of a recent California-wide assessment of organic agriculture, this paper argues that efforts intended to spur growth in the sector have multiple, sometimes paradoxical outcomes. Using the Drivers-Pressures-State-Impact-Response (DPSIR) diagnostic framework, we explain how market, environmental, and regulatory drivers create both positive and negative states within the system, which are fragmenting the organic agricultural innovation system and impeding advancements. Findings are organized into three main themes: (i) contradictions between the various philosophies of organic agriculture and the federal National Organic Program, (ii) contradictions between organic practices and other agricultural policies, and (iii) contradictions in the approach to technology and innovation. We discuss the importance of such causal diagnoses, potential policy responses to mitigating negative effects, as well as broader implications for the future of organic agriculture.</p>