The biochar application has been reported to have a positive effect on crop yield and nutrient utilization. However, the effects of the joint application of biochar and nitrogen (N) on soil physical properties, fruit yield, quality, crop water productivity (WP) and partial factor productivity of nitrogen (PFPN) of water-stressed greenhouse tomato under drip fertigation remain poorly understood. In this study, a two-season experiment was conducted on greenhouse tomato in autumn 2021 and spring 2022, involving two biochar application rates (0 and 30 t ha–1 only in the frst season before sowing), two N fertilization rates (175 and 250 kg N ha–1), and three irrigation levels (100%, 75%, and 50% of crop evapotranspiration). The results showed that biochar application signifcantly decreased soil bulk density by 7–13%, but signifcantly increased soil porosity by 5.5%− 10% and fruit yield by 43.2–73.8% compared with the non-biochar treatment. The biochar application signifcantly affected the total soluble solids (TSS), soluble sugar (SS), and vitamin C of tomato fruits. The interaction of biochar application and N fertilization increased PFPN and WP by 67.4% and 76.3% in autumn 2021, and by 38.1% and 51.8% in spring 2022, respectively. Biochar rate and irrigation level had signifcant effects on TSS and SS contents in both seasons, but N rate signifcantly affected TSS in autumn 2021 only and SS in both seasons. The interaction of biochar application, N rate and irrigation level had signifcant effects on fruit yield. The effects of biochar rate, N rate, and irrigation level on PFPN were signifcant in both growing seasons. The joint application of biochar and nitrogen signifcantly enhanced fruit yield, quality and water-nitrogen productivity of water-stressed greenhouse tomato. The Principal Component Analysis (PCA) revealed that PC1 accounted for 47.7% and 48%of the variation in autumn 2021 and spring 2022, while PC2 accounted for 14.6% and 15.6% in autumn 2021 and spring 2022, respectively. This study underscores the signifcance of biochar application in drip-fertigated greenhouse tomato cultivation and highlights its sustained positive effects in the next growing season.