Under intensive vegetable production, increased productivity is primarily considered for selecting better water management and irrigation intensity in upland soils. Soil water potential at −30 kPa (field capacity) for red pepper (Capsicum annum L.) production, which is the optimum moisture potential for plants, is recommended for Korean upland soils to maximize fruit yield; however its impact on greenhouse gas (GHG) emissions have not yet been considered. In this study, red pepper was cultivated under two soil water potentials at −30 and −50 kPa by drip irrigation control in two different textured soils (clay and sandy loams). Nitrous oxide (N2O) and methane (CH4) emissions were simultaneously investigated during the cultivation period. Results indicated N2O was the main GHG and contributed to approximate 97–9% of the total global warming potential (GWP), though the extent of its contribution varied depending on soil texture and soil moisture control with emitted CH4 being negligible throughout the investigation period. Between the treatments, soil moisture control at −50 kPa was effective in reducing the emissions of the two GHGs and also increased red pepper productivity in both clay loam and sandy loam soils. Comparing the gross GWP per unit pepper fruit yield between the treatments, maintaining soil water potential at −50 kPa by controlled irrigation led to a 50% reduction of GWP per unit pepper fruit yield. Therefore, drip irrigation control to lower soil water potential at −50 than −30 kPa is recommended to obtain high crop yield and reduce GWP per unit red pepper fruit yield for red pepper production in Korea.