Background <p>Photosynthetic activity in plant stems, particularly in woody plants and shrubs, is well known and documented. Nevertheless, our knowledge about the role of photochemical processes occurring in the stems of cultivated plants and their contribution to plant growth and development, including the root system, still remains unclear. Therefore, this study aims to determine the role of cells equipped with chloroplasts and located in the stems of tomato (<i>Solanum lycopersicum</i> L.) plants and whether changes in the activity of the photochemical processes affect the development of the plant’s root system and aboveground organs.</p> Results <p>The described study was conducted on tomato plants with stems covered with a doubled agrotextile (DP) that absorb 99% of incident light and on plants growing without coverage (NDP). Stem darkening led to the changes in the intensity of photochemical processes in these organs - a decrease in both the maximum and actual photochemical efficiency [F_v/F_m and Y(II)], as well as an increase in energy dissipation, both controlled (NPQ – non-photochemical quenching) and uncontrolled [(Y(NO) - non-regulated energy dissipation in photosystem II] way. These changes correlate with alterations in the anatomy of the stem cross-section. Darkening led to an increase in stem surface conductance to water vapour but a decrease in stem CO₂ efflux. The root length and dry mass of DP plants were significantly reduced compared to the roots of NDP plants. No significant differences were observed for the shoots (leaves + stems). The substantial changes in the structure of chloroplasts located in the stem cells of DP were also observed, with visible signs of ageing and disintegration of these organelles. In addition, the composition of the nitrogen forms in the soil where the plants were grown was different between DP and NDP. The soil from DP plants showed a higher total nitrogen content; however, unlike the ammonium and nitrate forms (NH₄⁺ and NO₃⁻), the nitrite form (NO₂⁻) was present at a lower concentration in this substrate compared to that of the NDP plants. Darkening did not have a direct effect on the δ¹³C and δ¹⁵N composition between NDP and DP plants, nor on the carbon-to-nitrogen ratio in the leaves, roots, and stems. Nevertheless, based on the obtained results for δ¹³C, δ¹⁵N, and the nitrogen-to-carbon ratio, some general trends can be observed.</p> Conclusions <p>The obtained results suggest that photochemical processes occurring in tomato stems have an important influence on the development of the tomato plant, especially on the root system. Limited light access to the stems restricts root system growth and development, but shows no visible negative effects on the above-ground parts of the tomato plants in this study. However, indirect effects on shoot growth and development cannot be excluded. Restricting light exposure to the stems likely reduces energy production in the form of energy carriers, such as ATP and NADPH, resulting in decreased efficiency of assimilate transport to the root. This disrupts the plant’s nitrogen uptake and balance, and in turn limits root system development. Moreover, it can be assumed that the chloroplasts present in tomato stems differ structurally and, as a consequence, functionally from those in leaves, which are specialised for efficient photosynthesis. Because a well-developed root system is an important factor affecting plant growth and yield, the obtained results may suggest the possibility of agronomic practices aimed at increasing the efficiency of photochemical processes and photosynthesis in the stems, and consequently improving yields.</p>