Transplants of angelica (Angelica archangelica L.), horehound (Marrubium vulgare L.), and thyme (Thymus vulgaris L.) were grown in multicompartment trays with five proportions of compost (0%, 15%, 30%, 45%, 60%) mixed to peatmoss and perlite. Plants were fertilized with different electrical conductivity (EC) levels of the nutrient solution (0, 1, and 2 mmho/cm). Horehound and thyme plants were transplanted in the field to measure the residual effects of treatments on dry matter yields and level of active substances. The three medicinal plants showed increased shoot and root dry weights as well as leaf mineral content (some nutrients) when proportion of compost and EC of nutrient solution were higher. The optimal combinations of compost and fertilization treatments on plants growth varied between species. Residual effects of treatments applied in greenhouse on shoot dry matter weight of horehound and thyme plants were observed until the 9th and 12th week, respectively, after transplantation. Treatments also affected active substance levels in horehound plants in field. Organic fertilization management influenced growth, yield in the field and level of certain active substances of the harvested parts of medicinal plants.