In recent decades, agriculture has been typified by a reliance on synthetic pesticides, with detrimental effects on human health and the environment. It has therefore become necessary to develop more sustainable pest management strategies. To meet this objective, agricultural practices within innovative cropping systems are designed to reduce synthetic pesticide inputs, while controlling pest and pathogen life cycles. However, knowledge is still needed when it comes to the ways in which consecutive growing seasons characterized by lighter synthetic pesticide inputs affect long term crop damage by pests and pathogens, and how their minimal use can cascade on the harvested yield. This article presents a longitudinal comparison, over five years, of the severity of Septoria leaf blotch and harvested yield of winter wheat cultivated with and without synthetic pesticides among one conventional and three innovative systems – low-input-, conservation-, and organic agriculture. Conventional and conservation agriculture systems showed, respectively, the highest and the lowest difference in Septoria severity between untreated winter wheat and the same crop treated with synthetic pesticides, making them the most and least chemical protection-dependent systems. The four cropping systems produced different yields, which were not significantly influenced by the reduction in synthetic pesticide input. Low-input agriculture proved to be the best trade-off between minimal synthetic pesticide use and Septoria severity, with no effect on yield. Our study provides evidence that adopting innovative cropping systems that are less dependent on synthetic pesticides, and thus contributing to a sustainable agriculture for the future, can be done without missing production targets.