<p>Nitrogen (N) fertilization improves crop productivity. However, the long-term effects of N application on methane (CH₄) emissions in drained peat soils, particularly under different hydrological conditions, remain poorly understood. Accurate quantification of CH₄ emissions from peatlands is essential for assessing carbon losses and formulating effective climate change mitigation strategies. This study was conducted to investigate the impact of N fertilization on CH₄ emissions and identify the main factors influencing CH₄ emissions from drained tropical peatlands. This study was conducted on an oil palm plantation in Sarawak, Malaysia, a randomized block design included four N fertilizer treatments: Control (0&#xa0;kg N ha^− 1 yr^− 1) (T1); low (31.1&#xa0;kg N ha⁻¹ yr⁻¹) (T2), moderate (62.2&#xa0;kg N ha⁻¹ yr⁻¹) (T3), and high (124.3&#xa0;kg N ha⁻¹ yr⁻¹) (T4). Soil CH₄ fluxes showed no statistically significant differences between treatments or across years, with emissions ranging from − 163.6 to 320.7&#xa0;µg C m^− 2 hr^− 1 at T1, -86.7 to 285.8&#xa0;µg C m^− 2 hr^− 1 at T2, -131.6 to 274.1&#xa0;µg C m^− 2 hr^− 1 at T3 and − 125.7 to 185.9&#xa0;µg C m^− 2 hr^− 1 at T4 (<i>p</i> &gt; 0.05). Although ammonium sulfate fertilization did not significantly alter CH₄ emissions, its pronounced acidifying effect on soil pH, particularly at application rates above 62.2&#xa0;kg N ha⁻¹ yr⁻¹ along with elevated sulfate (SO₄²⁻) inputs and nitrogen pools exceeding the critical threshold (&gt; 400 ppm), likely suppressed methanogenic activity and constrained soil organic matter decomposition. Water-filled pore space (WFPS) influenced CH₄ emissions more than groundwater level (GWL), with the low GWL at the site limiting its impact. Increased WFPS (60–80%) reduced nitrate (NO₃⁻) through enhanced denitrification, lowering its inhibition on CH₄ production and thus increasing emissions. This study highlights the key role of soil moisture and nitrogen cycling in regulating CH₄ emissions in peatland.</p>