Magnesium (Mg) is one of the significant macronutrients which is involved in the structural stabilisation of plant tissues and many enzymes such as PSII. The latter efficiency and performance were analysed, using chlorophyll (Chl) a fluorescence induction kinetics and microscopic images, to detect the changes in structure and function of photosynthetic apparatus of radish plants grown under Mg deficiency (Mgdef). Plants grown under Mgdef showed less PSII connectivity and fewer active primary electron acceptors (QA) oxidizing reaction centres than control plants. Confocal and electron microscopy analyses showed an increased amount of starch in chloroplasts, and 3,3'-diaminobenzidine (DAB)-uptake method revealed higher H2O2 accumulation under Mgdef. Prominent changes in the Chl a fluorescence parameters such as dissipated energy flux per reaction centre (DIo/RC), relative variable fluorescence at 150 µs (Vl), and the sum of the partial driving forces for the events involved in OJIP fluorescence rise (DFabs) were observed under Mg deficiency. The latter also significantly affected some other parameters such as dissipated energy fluxes per cross-section (DIo/CSo), performance index for energy conservation from photons absorbed by PSII antenna until the reduction of PSI acceptors (PItotal), and relative variable fluorescence at 300 µs (Vk). This work emphasises the use of chlorophyll fluorescence in combination with microscopic and statistical analyses to diagnose the effects of nutrients deficiency stress on plants at an early stage of its development as demonstrated for the example of Mgdef. Due to the short growth period and simple cultivation conditions of radish plant we recommend it as a new standard (model) plant to study nutrients deficiency and changes in plant photosynthetic efficiency under stress conditions.