Rapidly warming climate, tightening environmental requirements, an aging society, rising wages, and demand for organic products are forcing farming to be more efficient and sustainable. The main aim of this study was to perform an analytical analysis and to determine the energy use and GHG emissions of organic sugar beet production using different weed control methods. Seven different methods of non-chemical weed control were compared. Mechanical inter-row loosening, inter-row cutting and mulching with weeds, weed smothering with catch crops, and thermal inter-row steaming were performed in field experiments at the Experimental Station of Vytautas Magnus University (Lithuania, 2015–2017). The other three, namely, automated mechanical inter-row loosening with cameras for row-tracking, inter-row loosening with a diesel-powered robot, and inter-row loosening with an electric robot were calculated analytically. The results showed that the average total energy use of organic sugar beet production was 27,844 MJ ha−1, of which manure costs accounted for 48–53% and diesel fuel for 29–35%. An average energy efficiency ratio was 7.18, while energy productivity was 1.83 kg MJ ha−1. Analysis of GHG emissions showed that the total average GHG emissions to the environment from organic sugar beet production amounted to 4552 kg CO2eq ha−1, and the average GHG emissions ratio was 4.47. The most sustainable organic sugar beet production was achieved by using mechanical inter-row loosening with a diesel-powered robot for weed control.