Agricultural management, environmentally friendly technologies, chemical, organic and bio-based substances used, as well as meteorological factors, have a significant impact on the fluctuations of soil organic carbon (SOC). The aim of this research was to analyze the effect of different biopreparations on the changes of SOC content and the winter wheat and winter oilseed rape yields by assessing the energy consumption efficiency and the environmental impacts. The experimental research was conducted from 2017 to 2019 in three different treatments, in two of which were used either a molasses and magnesium sulphate based-biopreparation (T1) or a bacteria-based biopreparation (T2), while treatment T3 was applied as a control where no biopreparations were used. The dynamics of SOC content were analyzed at two depths: 0–10 and 10–20 cm. For the analysis of energy efficiency indicators and environmental impacts, the greenhouse gas (GHG) and energy consumption conversion equivalents were used. A summary of the results showed that both types of biopreparations had a positive effect on the changes of SOC content, which was especially evident in the deeper layers at 10–20 cm depth, where, irrespective of the crop type, a more significant increase of the SOC content was observed every year of the experiment compared to the control treatment. Biopreparations had a significant effect in increasing the winter wheat and winter oilseed rape yield. The best energy efficiency ratio was observed in winter wheat (4.84) and winter oilseed rape (5.11) in treatment T1. The results of the environmental impact assessment showed that the lowest GHG emissions were recorded in the winter wheat production in treatment T1 at 108.7–149.1 kg CO2eq Mg−1, while the highest were observed in oilseed rape production in the control treatment T3 at 343.4 kg CO2eq Mg−1.