Casuarina equisetifolia plantations have been widely established along tropical and subtropical coasts, where they act as a windbreak to shelter coastal areas. These shelter plantations also fulfill important ecosystem service by sequestering large amounts of carbon (C). However, shelter plantations are usually established on nutrient-poor sand dunes, which may limit tree growth and therefore C sequestration rates. To assess whether fertilization increases the C sequestration of coastal shelter plantations, we conducted a fertilization experiment in a young C. equisetifolia plantation with four treatments: nitrogen addition (+N), phosphorus addition (+P), nitrogen and phosphorus addition (+NP), and controls (CK). We quantified nutrient availability and annual net ecosystem production (NEP) during the key early establishment phase. Fertilization with +N and + P significantly increased ammonium-N and extractable P in the surface soils and the N and P concentrations of branches, respectively. Surprisingly, the mean growth rate of C. equisetifolia plantations (24.59 ± 0.66 Mg ha−1 yr−1) was not affected by fertilization. The mean NEP was 6.18 ± 0.49 Mg C ha−1 yr−1, and there was no difference among fertilization treatments. However, soil organic C significantly increased by 41% and 36% with +N and + P, respectively, but not +NP. C. equisetifolia plantations can sequester large amounts of C in biomass on poor soils without the need for additional nutrients, although fertilization may enhance soil C storage. Considering the potential large planting area, we suggest that coastal C. equisetifolia shelter plantations could be an important nature-based solution for climate change mitigation in coastal regions.