Indonesia is one of the world's economies contributing the most to greenhouse gas (GHG) emissions from the global food system. This study aimed to quantify the environmental impacts of Indonesian vegetable production and the relative contribution of different farm inputs. Data were collected from 322 vegetable farms in the Lembang sub-district in West Java. A Life Cycle Assessment (LCA) was carried out to estimate global warming potential (GWP), acidification potential (AP), freshwater eutrophication potential (EP), and abiotic resource depletion. Results of the LCA showed that GHG emissions were 14.1 t CO2eq ha−1 yr−1 (0.5 t CO2eq t−1), AP was 39.3 kg SO2eq ha−1 yr−1 (1.4 kg SO2eq t−1), EP was 45.3 kg PO4eq ha−1 yr−1 (1.7 kg PO4eq,), and depletion of phosphate, potash, and fossil fuel resources were 60.0 kg P2O5, 101 kg K2O, and 6299 MJ ha−1 yr−1, respectively (1.9 kg P2O5, 3.7 kg K2O, and 281 MJ t−1). Organic fertilizer use contributed the most to impact categories of global warming, freshwater eutrophication, and acidification, followed by synthetic fertilizer. The sensitivity analysis showed that yield and organic fertilizer use explained most of the variation in GHG emission per ton product. Therefore, it is recommended to include organic fertilizer use in the fertilizer advisory system for vegetable production in Indonesia.