Agriculture uses a lot of fuel, fertilizers, pesticides and other substances, while emitting large amounts of GHGs. It is important to optimize these inputs and outputs. One such way is by increasing crop biodiversity. For this reason, single crops and mixtures of maize, hemp and faba bean as binary and ternary crops were investigated at the Experimental Station of Vytautas Magnus University, Lithuania. The results showed that consumption of diesel fuel was 31–46% higher than in single and 22–35% higher than in binary cultivations was found in a ternary crop. This had influence on the highest energy input of near twice higher than in maize and hemp single crops and maize+hemp binary crop, but similar with binary crops with faba bean. Despite this, the productivity of the ternary crop and, at the same time, the energy output were 2–5 times higher than in other treatments. This compensated for higher energy inputs and the energy efficiency ratio. In the ternary crop, energy productivity was from 1.1 to 2.8 times higher and net energy was 1.9–5.3 times higher than in other tested cultivations. The highest total GHG emissions were obtained in binary maize+hemp and maize+faba bean cultivations (1729.84 and 2067.33 CO2eq ha−1). Ternary cultivation with the highest energy inputs initiated average GHG emissions of 1541.90 kg ha−1 CO2eq. For higher efficiency, the ternary crop could be sown and harvested in one machine pass. Faba beans should be included in ternary crops, as their biomass makes up a significant part of the total biomass produced. We recommend reviewing the intercropped faba bean seeding rates, as faba bean seeds have a high energy input equivalent.