Acid-sulfate soils and overuse of chemical fertilizers have been obstacles to sustainable agriculture. The variation of fertilization due to poor soil fertility has remarkably affected the yield gap and the quality of the environment, so an optimal fertilizing rate should be formulated. Therefore, this study was aimed at (i) detecting obstacles in soil characteristics reducing pineapple yield between farms and (ii) assessing the effects of NPKCaMg fertilizers on soil fertility, uptakes, and pineapple yield. The on-farm experiment was carried out according to site-specific nutrient management (SSNM) arranging in acid-sulfate soil for pineapple, including (i) no fertilizers used; (ii) NPKCaMg: fully fertilizing with nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg); (ii) PKCaMg: fertilizing without N; (iii) NKCaMg: fertilizing without P; (iv) NPCaMg: fertilizing without K; (v) NPKMg: fertilizing without Ca; (vi) NPKCa: fertilizing without Mg; and (vii) FFP: farmers’ fertilizing practice. The result of the principal component analysis revealed that the soil had low availability of N, P, and K nutrients. Available P concentration was negatively correlated with concentrations of Al³⁺, Fe²⁺, and total Mn, whose correlation coefficients were -0.34 to -0.59, -0.52 to -0.74, and -0.63 to -0.70, respectively. Fertilizing NPKCaMg obtained the highest result in the uptakes of N, P, K, Ca, and Mg, which were 289.1–327.4, 25.4–29.3, 137.4–166.0, 41.9–48.9, and 39.8–43.1 kg ha^-1, respectively. Fertilizing by SSNM has increased pineapple yield by 22.9%–44.9% compared to the FFP. This fertilizer formula should be transferred to the local farmers in order not only to enhance productivity, but also to limit the damage of chemical fertilizers on the environment. Moreover, this formula should be tested globally in other places that share similar soil characteristics.