This study aimed to assess the effect of using selected herbs as companion crops in soybean cultivation on the yield and overall health of soybeans. A three-year field experiment (2021–2023) was conducted using a randomized block design with three replications, where the primary experimental variable was the sowing method. The innovative cropping system involved cultivating soybeans alongside different companion herbs, such as alyssum (Lobularia maritima L.), fennel (Foeniculum vulgare Mill.), borage (Borago officinalis L.), French marigold (Tagetes patula L.), calendula (Calendula officinalis L.), and a herbal mixture referred to as ‘MIX’. The study showed that cultivation of soybean with fennel improved the quantitative and qualitative characteristics of the yield, with a significant increase in seed yield (on average by 0.27 t ha−1) as well as protein (7.67%) and oil yield (8.57%) compared to the pure soybean crop. The following fungal diseases were identified during the three-year study period (2021–2023): Cercospora leaf blight, Ascochyta blight, Fusarium wilt, and downy mildew. Cultivation of soybean with herbs as companion crops was implemented to improve the health of soybean to a varied extent. Borage, marigold, and calendula companion crops reduced infection of soybean by the fungi C. kikuchii and F. oxysporum. Cultivation with fennel and marigold was also beneficial for soybean health. On the other hand, cultivation with sweet alyssum and a mixture of herbs increased the occurrence of the fungus A. sojaecola. Cultivation of soybean in association with herbs is legitimate and requires further research given the priorities facing 21st-century agriculture.