Trees and soil management practices (i.e., pruning and fertilization) are essential in maintaining the soil fertility and coffee yield sustainability in coffee agroforestry systems. This study aimed to evaluate the impact of trees and soil management practices on the soil nutrient status within coffee-based agroforestry systems. The research was conducted in coffee agroforestry systems within Universitas Brawijaya Forest (UB Forest) from January to July 2023. The experiment was performed using a factorial randomized block design with three factors, including: 1) pruning of coffee (T1: pruned coffee, T2: unpruned coffee), 2) Fertilizer type (O: organic fertilizer, A: inorganic fertilizer, M:50% organic + 50% inorganic), and 3) Fertilizer dosage (D1: Farmer‘s dose, D2: recommended doses from the Indonesian Coffee and Cacao Research Institute (ICCRI), D3: Dosage from nutrient replacement), totaling 18 treatments with four replications of each. The soil sample was collected at topsoil (20 cm soil depth) around 50 cm from the coffee stem at the beginning of the research and six months after fertilization. The study revealed that tree management affected (p>0.05) soil nutrient status (i.e., soil total N and available P), where pruned coffee management increased soil nutrient status by 2.02 to 4.53 times compared to the unpruned coffee plot. Types and doses of fertilizer significantly affected soil pH (P < 0.05), where the application of organic fertilizer with the recommended dose (OD2) had the highest soil pH. The correlation analysis showed that soil nutrients correlated to coffee yield. The principal component analysis shows that pruned coffee combined with mixed fertilizer at the farmer‘s dose (T1MD1) is closely related to coffee production.