The partial substitution of chemical nitrogen fertilizers with organic fertilizer and slow-release fertilizer could improve pineapple yield and nitrogen use efficiency (NUE) and decrease greenhouse gas (GHG) emissions. However, the effect of organic and slow-release fertilizer substitution strategies on the carbon footprint (CF), nitrogen footprint (NF) and net ecosystem economic benefits (NEEB) from pineapple fields in the tropics remains largely unclear. Therefore, we conducted a long-term pineapple field trial (2017–2021) for the first time with five fertilization strategies (CK: no fertilizer; F: conventional fertilization(nitrogen (N) 817 kg ha⁻¹, phosphorus pentoxide (P₂O₅) 336 kg ha⁻¹, potassium oxide (K₂O) 945 kg ha⁻¹); RF: reduction of 41.7% N, 72.0% P₂O₅ and 33.1% K₂O on an F basis; RFO: replacement of 20% N input with organic fertilizer on an RF basis; RFOS: replacement of 15% N input with slow-release fertilizer on an RFO basis) to identify the pineapple fruit yield, NUE, CF, NF and NEEB in the tropics. The results showed that in comparison to the F treatment, the RF, RFO and RFOS treatments improved pineapple yield (7.6%, 12.4% and 26.3%, respectively), NUE (66.4%, 75.5% and 87.7%, respectively, p < 0.05) and partial factor productivity of nitrogen (PFP_N) fertilizer (84.8%, 92.8% and 116.7%, respectively, p < 0.05). Additionally, of all the treatments, the RFOS treatment had the highest yield (87.8 t ha⁻¹). N leaching (50.1–69.1%) and ammonia volatilization (21.6–26.2%) were the two primary routes for reactive nitrogen (Nr) loss. The field soils (36.8–45.7%) and N fertilizer production and transportation (21.2–29.5%) dominated the GHG emissions. Compared to the F treatment, the RF, RFO and RFOS treatments showed decreases in Nr losses, NF, GHG emissions and CF of 36.6–41.1%, 43.3–51.9%, 19.0–29.1% and 24.5–41.7%, respectively. Of all the treatments, the RFOS treatment had the lowest CF (191.8 kg CO₂eq ha⁻¹ season) and NF (1.9 kg N t⁻¹ season). Additionally, the NEEB of the RF, RFO and RFOS treatments improved by 13.0–39.9% over that of the F treatment. The RFOS treatment (54,880 USD ha⁻¹) resulted in the highest NEEB of all treatments. Therefore, the substitution of conventional inorganic fertilizers with organic and slow-release fertilizers is an effective method for achieving sustainable pineapple production. However, a process for further reducing GHG emissions from farmland soils and Nr losses from organic fertilizer addition still need attention in terms of pineapple production.