Abstract Climate change, increasing energy demand, and fossil fuel constraints have led to many plights regarding sustainable food and agricultural production. The purpose of this paper is to assess of exergoenvironmental aspects across different paddy production systems, including conventional (CS), low external input (LEI), and organic systems (OS) in Iran. Also, life cycle cost (LCC) and the emissions costs have been considered as a novelty for these scenarios. Data were collected through interviews from 213 paddy producers. Environmental life cycle damages were assessed by IMPACT 2002+ based on 1 ton of paddy yield as the functional unit. The findings revealed that diesel fuel followed by nitrogen had the most substantial role in the resource damage category of CS and LEI, while most values of OS belonged to diesel fuel followed by electricity. Furthermore, On-Farm emissions claimed almost the largest share among the other impacts categories in the surveyed systems. The cumulative exergy demand (CExD) analysis indicated that Non-renewable, fossil fuel was the main energy consumer. In this regard, diesel fuel was the most substantial part of energy forms for all three systems reducing the total CExD. The economic analysis showed that the lowest LCC was associated with OS; accordingly, the highest net profit belonged to OS, followed by CS. Overall, it can be concluded that the advantage of the OS scenario is evident for long-term management and planning in different environmental-exergy-economic indices of production systems.