Weed control is one of the most important technological operations to ensure crop yield and quality in ecological sugar beet production. However, conventional mechanical weed control is labor- and time-intensive and has adverse effects on the soil and the environment. The aim of this study was to experimentally investigate the influence of conventional mechanical and robotic weed control systems on soil properties and to assess the effectiveness of these different weed control methods in ecological sugar beet production. This study examines two different weed control systems: robotic weed control (RWC) and conventional weed control (CWC). Field experimental studies were carried out with a solar-powered field robot and conventional inter-row cultivation (CWC1—first cultivation, CWC2—second cultivation) to determine the effectiveness of mechanical weed control in ecological sugar beet crops. The influence of different weed control systems on the physical properties of the soil in the contact zone between the soil and the tires of weed control machines was investigated. The results showed that the average weed control effectiveness inter-row was higher in the RWC (81%) compared to that in the CWC2 (46%). The overall weed control effectiveness of the robotic weed control in the sugar beet inter-row and intra-row was around 49%. The measurements showed that the weed control process reduced the soil moisture and temperature in all treatments tested. Experimental studies have confirmed that the weed control operation, although carried out with relatively lightweight robots, also has an impact on soil bulk density. RWC weed control resulted in an average increase of 0.16 g cm^–3 in soil bulk density in the topsoil layer (0–10 cm) after weeding. Both CWC1 and RWC increased soil penetration resistance (PR). For CWC1, the average increase in topsoil PR after weed control was 20%, while for RWC, the increase was marginal, only around 1%. Automated precision weed control by self-propelled solar-powered field robots is an important solution to reduce the need for tedious and time-consuming manual weeding.