This study evaluated weed infestation and health of the soybean crop grown in crop rotation (CR) and monoculture (CM) under conventional tillage (CT) and no-tillage (NT) conditions. The research proved that growing soybean in monoculture and under no-tillage conditions increases weed infestation and infection of soybean with fungal diseases. In these treatments, increased numbers of most of the dominant species were also found. A significantly higher percentage of monocotyledonous species and a much lower percentage of dicotyledonous ones in total weed dry weight were shown in the CR treatment relative to CM and in the NT system compared to CT. The biodiversity of the weed community was similar in monoculture and crop rotation, and slightly greater in the NT system in comparison with CT conditions. In both tillage systems, Amaranthus retroflexus was the weed species that most infested the soybean crop. In soybean grown after itself, Amaranthus retroflexus was the weed that occurred in the greatest numbers, while, in crop rotation, this was Echinochloa crus-galli. In all years of the study, soybean was infected with Septoria glycines to the highest degree, which was followed by Cercospora sojina, whereas infection with Ascochyta sp. was the lowest. Weather conditions in individual years of the study were proven to affect weed infestation and infection of soybean with fungal diseases. The study results prove that cropping systems and tillage systems significantly affect weed infestation and health of the soybean crop.