Chenopodium quinoa Willd. is an annual facultative halophytic pseudocereal widely studied for its physiology and grain yield owing to its great tolerance to unfavorable growing conditions. However, the morphophysiological and anatomical characteristics of plants’ photosynthetic organs under various and combined abiotic stresses during the early stages of development have not been thoroughly studied. Therefore, the current study compared the influence of osmotic, salt, and combined stress at different intensities on the morphology and anatomy of photosynthetic organs in young quinoa plants. The main findings demonstrate that salt stress at an intensity between 100 and 200 mM NaCl is not critical for the growth of young quinoa plants and that the young plants can withstand salt stress at an intensity of 300 mM NaCl. However, it can be concluded that some adaptation mechanisms of the plants were already violated at a salt stress intensity of 200 mM NaCl, while significant changes in the water balance of the plants were observed at an intensity of 300 mM NaCl, possibly caused by damage to the cell structures.