Biologically active compounds are key-important ingredients of tomato fruits, especially those produced by organic agricultural practices. Being biologically effective soil treatments, microbial inoculants can improve soil quality through a variety of mechanisms. Their activity can influence soil properties and plant development, thereby determining the quantity and quality of the crop. However, little research was done on how these inoculants affect the nutritional quality of the tomato fruit and on the antioxidant status of the fruits. This study investigated lycopene content and total antioxidant capacity of organically grown tomato fruits (Solanum lycopersicum L. var. ‘Mobil’) using various types of single and combined bioeffector products in two growing seasons. Single inoculation contained Trichoderma harzianum, plant growth promoting Pseudomonas sp., and phosphorus-mobilizing Bacillus amyloliquefaciens strains. The combined treatment consisted of biotic Trichoderma harzianum, Pseudomonas fluorescens, and Bacillus subtilis strains with abiotic micronutrients of zinc and manganese. Sum of ranking differences method, as a multicriteria optimization method, was used to rank the treatments and identify the ones deviating the least from the reference treatment. The results showed that all microbial soil inoculants positively affected tomato lycopene content. The combined treatment showed significantly higher lycopene content than the Control in both years. We found that weather and climate conditions also greatly influence the total antioxidant capacity. Based on our results, we recommend the use of combined bioeffective treatments to improve the food quality value of tomato fruits.