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Plant diversity can have a profound impact on disease dynamics, with important applications for enhancing sustainability. Disease is often reduced by intercropping, but variability can be high. This study investigated integration of several management approaches to stabilize this variability for early leaf spot (ELS) and late leaf spot (LLS) of groundnut, over seven seasons in three phases. In phase 1, monocrops and alternating row and strip intercrops with maize were artificially inoculated with ELS in an area with little groundnut production. Reductions in AUDPC of 37–73% in strip treatments compared to monocrops prompted testing of the efficacy of intercropping in intensive production areas for phases 2 and 3. Additional treatments included cotton strip intercrops, and integration of intercropping with reduced fungicide treatments and partial resistance to leaf spots. In phase 2, the use of cotton strip intercrops lowered natural ELS epidemics by 25–41% (AUDPC) through delayed disease onset, but maize had inconsistent effects. Intercropping was not effective against LLS, which dominated in phase 3. Reduced fungicide regimes and partial resistance lowered disease, and in one case interacted with intercropping to enhance disease suppression. Groundnut yields generally were inversely proportional to disease levels and not significantly reduced by intercropping. Separate studies to determine maize impacts on ELS infection implicated disruption of dispersal as the mechanism of disease reduction. This work demonstrates that intercropping may be most effective where low levels of ELS are present, using strip patterns with cotton, and combined with other tools such as resistance and reduced fungicide application.