In this study, a comparative economic analysis was conducted for typical greenhouses, plant factories with natural and artificial light, and those with only artificial light, based on the insulation, artificial light, and photovoltaic (PV) installation costs. In addition, the results of research on primary energy consumption and greenhouse gas (GHG) emissions from the use of fossil fuels were presented. By comparing the case-wise annual energy consumption, when all energy sources were converted into primary energy consumption based on the applied coefficients for collection, transport, and processing, to unify calculations for different fossil fuel energy sources, the case of the installed PV systems exhibited large reductions, of 424% and 340%, in terms of primary energy consumption and GHG emissions, respectively. Furthermore, electric heating resulted in higher primary energy consumption and GHG emissions than oil. When the economic analysis included the plant factory installation cost used to maintain the temperature required for plant growth in winter, the PV installation exhibited the highest cost; additionally, all plant factories showed an investment payback period of seven to nine years, which is comparable to typical greenhouses. Based on these results, we aim to reduce the use of fossil fuels for sustainable energy by combining architectural technology for improved energy performance in the agricultural environment.