It is crucial to determine energy efficiency and environmental effects of greenhouse productions. Such study can be a viable solution in probing challenges and existing defects. The aims of this study were to analyze energy consumption and greenhouse gas (GHG) emissions for pepper production using biological method inside greenhouses which used natural gas (NG) heating system in Esfahan province. Data were collected from 22 greenhouse holders using a face to face questionnaire method, in 2010-2011. Also, functional area was selected 1000 m2. Total energy input, total energy output, energy ratio, energy productivity, specific energy, net energy gain and total GHG emissions were calculated as 297799.9 MJ area-1, 3851.84 MJ area-1, 0.013, 0.016 kg MJ-1, 61.85 MJ kg-1, -293948 MJ area-1 and 14390.85 kg CO2 equivalent area-1, respectively. Result revealed that replacing diesel fuel with NG will not be an effective way of reducing energy consumption for greenhouse production. However, it is crucial to focus on energy management in order to enhance the energy and environmental indices. One way to supply adequate input energy and a reduction in GHG emissions is the utilization of renewable and clean energy sources instead of NG and diesel fuel. Also, it is suggested to adopt solar greenhouses in the region and to supply electricity from non-fossil sources seriously.