Soil treatments have a significant influence on the agricultural and environmental productivity of agricultural practices. Arable lands are one of the sources of greenhouse gas emissions (GHG) that are influenced by the chemical and physical properties of the soil and are an essential contributor to climate change. We aim to evaluate the long-term management of agricultural practices, such as different tillage systems, cover crops, and glyphosate, on GHG emissions and soil physical properties. The field trial involved three tillage systems (conventional tillage (CT), reduced tillage (RT), and no-tillage (NT)), along with variations in cover cropping (with and without cover crops) and glyphosate application (with and without glyphosate). These treatments were implemented during the cultivation of oilseed rape in 2022 as part of a cropping sequence consisting of five crops: winter wheat; winter oilseed rape; spring wheat; spring barley; and field pea. Greenhouse gas emissions (carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)) were directly measured using a closed static chamber system. Through the examination of these management techniques, the soil\u2019s physical properties over the studied period were assessed for their impact on GHG fluxes. The findings of the study reveal that N2O emissions were relatively low during the first month of measurement, with significant differences (p < 0.05) observed in the interaction between cover crop and glyphosate treatments. Additionally, N2O emissions were notably elevated in the reduced (0.079 \u00b5g m\u22122 h\u22121) and conventional tillage (0.097 \u00b5g m\u22122 h\u22121) treatments at the second month of measurement. Regarding CH4, increased emissions were observed in the reduced tillage and cover crop treatments. CO2 emissions exhibited variability across all of the investigated treatments. Notably, GHG fluxes spiked at the second measurement, signifying the maximum uptake of nutrients by the main plants during the growth phase. Greenhouse gas emissions leveled off across all of the treatments following the harvest, marking the end of the cultivation period. The influence of the deployed techniques varied across the determined physical parameters of the soil. The incorporation of cover crops contributed to improved water content and, further, to electrical conductivity. Glyphosate use showed no direct impact on physical properties of the soil while the different tillage treatments had varying effects on the distribution of the physical properties of the soil with respect to the degree of disturbance or tillage-induced changes. Additionally, GHG emissions were strongly correlated with precipitation at one week and two weeks before sampling, except for CO2, which showed a weaker correlation at two weeks before GHG sampling. The findings indicate that reduced and conventional tillage methods might adversely affect greenhouse gas emissions and plant functionality, particularly concerning nutrient release and uptake, especially in temperate climate conditions.