In this study, we investigated the effect of partially substituting inorganic nitrogen with bio-organic fertiliser on the ‘Tianhong2’ Fuji apple planting in Xinjiang. Bio-organic fertiliser was applied, and nitrogen was reduced by 20% (T2), 40% (T3), and 60% (T4) during the blooming and fruit expansion periods with conventionally fertilised fields used as control (T1); soil nutrient, soil enzyme activity, leaf nutrients, fruit quality, and yield were measured. The total nitrogen (TN), total phosphorus (TP), total potassium (TK), total calcium (TCa), available phosphorus (AP), available potassium (AK), and soil organic matter (SOM) contents, as well as the soil catalase (S-CAT), soil uretrase (S-UE), soil saccharase (S-SC), and soil nitrate reductase (S-NR) activities, significantly increased in the experimental soils compared with those in T1. In addition, TP, TCa, and total magnesium (TMg) content in apples significantly increased. Compared to T1, the T2 and T3 treatments significantly improved the fruit yield and quality, increasing the sugar–acid ratio, soluble protein, soluble sugar, peel carotenoid, and anthocyanin content and reducing peel chlorophyll content. The brightness (L*), red–green axis (a*), yellow–blue axis (b*), colour intensity (C), and tone (h°) values changed. The yield per hectare and nitrogen fertiliser partial productivity values were significantly increased. Overall, the T2 treatment resulted in the best outcome for the Yili area. In conclusion, partially substituting inorganic nitrogen with bio-organic fertiliser can effectively increase soil and leaf nutrient content and improve fruit yield and quality.