This dataset contains original research data from Gulu, Northern Uganda, for two growing seasons: Long rain season in 2023 and short rain 2023-2024. We investigated the effects of conventionally tilled systems under crop rotation (Conventional) versus continuous maize monocropping (ConventMM), as well as the effects of different tillage systems (Conventional, Conservation Agriculture (CA), and CA with biochar) under a pigeon pea–maize rotation on crop yield, soil N dynamics, and N₂O emissions.