We report the synthesis of twelve indole derivatives bearing nitro or amide groups via Fischer indole methodology followed by reduction/acetylation and amidation reactions. After thorough characterization, these indoles were subjected to a number of studies in order to evaluate their bioactive potential as photosynthesis and plant growth inhibitors. Firstly, these molecular hybrids were evaluated as photosystem II (PSII) inhibitors through chlorophyll a (Chl a) fluorescence measurement. In this study, 6‐chloro‐8‐nitro‐2,3,4,9‐tetrahydro‐1H‐carbazole (15a) and 5‐chloro‐2,3‐dimethyl‐7‐nitro‐1H‐indole (15b) showed the best results by reducing the phenomenological parameters of reaction centers ABS/RC, TR0/RC and ET0/RC of PSII. Electron chain blockage by these compounds may lead to diminished ATP synthesis and CO2 fixation which interrupt the plant development. The compounds 15a and 15b both act as postemergent herbicides, reducing the dry biomass of Ipomoea grandifolia and Senna alata weeds by an average of 40% and 37%, respectively, corroborating the fluorescence results. Additionally, the molecular docking study revealed that the presence of strong electron‐withdrawing groups at the indole phenyl ring is important for the ligand’s interaction with the binding pocket of protein D1 on PSII. The optimization of these molecular features is the goal of our research group in further understanding and development of new potent herbicides. This work reports the synthesis of indole nitrogen hybrids and their bioactive potential as photosystem inhibitors. The molecular hybrids were evaluated as photosystem II inhibitors through chlorophyll a fluorescence measurements and plant growth inhibitors. Compounds 6‐Chloro‐8‐nitro‐2,3,4,9‐tetrahydro‐1H‐carbazole and 5‐chloro‐2,3‐dimethyl‐7‐nitro‐1H‐indole showed the best results by reducing the phenomenological parameters of the reaction center, diminishing ATP synthesis and CO2 fixation which interrupt the plant development. Additionally, the molecular docking study revealed that the presence of strong electron withdrawing groups at the indole phenyl ring are important for the ligands’ interaction with the binding pocked of protein D1.