This study aimed to evaluate greenhouse gas (GHG) emissions from conventional cultivation (S1) of seedless lime (SL) fruit in Hau Giang province, in the Mekong Delta region of Vietnam. We adjusted the scenarios by replacing 25% and 50% of nitrogen chemical fertilizer with respective amounts of N-based organic fertilizer (S2 and S3). Face-to-face interviews were conducted to collect primary data. Life cycle assessment (LCA) methodology with the “cradle to gate” approach was used to estimate GHG emission based on the functional unit of one hectare of growing area and one tonnage of fresh fruit weight. The emission factors of agrochemicals, fertilizers, electricity, fuel production, and internal combustion were collected from the MiLCA software, IPCC reports, and previous studies. The S1, S2, and S3 emissions were 7590, 6703, and 5884 kg-CO2 equivalent (CO2e) per hectare of the growing area and 273.6, 240.3, and 209.7 kg-CO2e for each tonnage of commercial fruit, respectively. Changing fertilizer-based practice from S1 to S2 and S3 mitigated 887.0–1706 kg-CO2e ha−1 (11.7–22.5%) and 33.3–63.9 kg-CO2e t−1 (12.2–25.6%), respectively. These results support a solution to reduce emissions by replacing chemical fertilizers with organic fertilizers.