The aim of experiments was to assess the efficiency of choline-stabilized orthosilicic acid (ch-OSA; complex of orthosilicic acid with choline and a bioavailable source of silicon) application under increasing manganese (Mn) stress on the micronutritional composition and yielding of tomato (Solanum lycopersicum L. cvs. ‘Alboney F1’ and ‘Emotion F1’). Plants were grown in rockwool with the application of a nutrient solution varied the Mn concentrations (in mg dm−3): 9.6 and 19.2 which cause strong oxidative stress of plants comparing with optimal concentration of that microelement in nutrient solution. The effect of ch-OSA application (at Si concentration of 0.3 mg dm−3 nutrient solution) was investigated at both Mn-levels. Increasing Mn stress modified the concentration of microelements and silicon (Si) in tomato leaves. Application of ch-OSA also influenced the concentration of nutrients, but the determined changes were generally multidirectional and varied depending on Mn-level and cultivar. Under the increasing Mn stress a significant downward trend was observed for the mean concentration of Fe (in both cultivars) in fruits – but changes of Mn, Zn and Cu were varied depend on cultivar. In the case of cv. ‘Alboney F1’ ch-OSA application caused an increase the mean concentrations of Fe, Zn and Cu, while in the case of cv. ‘Emotion F1’ the reduction of mean concentrations of Zn and Cu was recorded. Ch-OSA treatment did not influence on the Mn concentrations in fruits. A beneficial role of ch-OSA was also found in photosynthesis activity. This was especially valid for lower levels of Mn. Application of ch-OSA improved significantly the marketable yield of tomato under stress by a low Mn level.