Nowadays, production and consumption of inputs play an important role in agri-food sectors. But applying inappropriate management of input consumption results in negative environmental repercussions and reduced economic profits. So conducting a comprehensive study on the production process of products in terms of energy input flow, economic costs and environmental impacts could play a key role in suitable input management on the whole production cycle. Accordingly, the present study aimed to conduct an energy-economic-environmental on onion production in two cropping systems including seeding and transplanting. Required data were collected from 4 different seeding systems in Isfahan region (55 questionnaires) and 5 different transplanting systems in Semirom-Buin regions (50 questionnaires). Based on the results, for seeding onion system, the total energy input varied between 2973 and 3938 MJ. tonne−1 for system (Ι) and (ΙΙΙ), respectively, while for transplanting system, it varied between 2218 and 2339 MJ. tonne−1 for system (IV) and (Ι), respectively. The average energy input for seeding and transplanting systems was obtained as 3579 and 2322 MJ. tonne−1, respectively. Electricity and diesel fuel were identified as the most consumed inputs in all systems. In terms of production costs, labor had the highest contribution to the total costs in seeding and transplanting systems with the amount of 12.73 (32%) and 25.22 $. tonne−1 (58%), respectively. Based on the results obtained from the analysis of energy and economic indices, the integrated index of Energy Intensiveness was obtained as 90.54 and 53.50 MJ $−1 for seeding and transplanting systems, respectively, which shows the high energy-economic efficiency of transplanting systems compared to the seeding systems. LCA results related to the environmental impacts of onion production showed that in seeding and transplanting systems, Global Warming (GW) and Environmental Final Impact (EFI) were obtained as 24.7 and 4.65 kg CO2.eq. tonne−1 and 15.42 and 4.22 pPt. tonne−1, respectively. Direct emissions caused by input consumption (CO2, NH3 and NO3−), and indirect emissions caused by electricity generation and manure production were identified as the environmental hotspots in onion production. In seeding cropping systems of (Ι) and (ΙΙ) which followed by the post-harvest processes, the total energy input, input costs and EFI index were determined as 3527 MJ, 74.37 $ and 13.18 pPt per one tonne of stored crop in the cold storage and 5458 MJ, 138.74 $ and 32.89 pPt per one tonne of processed onion in processing plant, respectively. Results related to the post-harvest operations highlighted the necessity of investigation of whole cycle of agricultural crops (cradle-to-grave analysis).