Drought is an abiotic scourge, one of the major environmental stress factors that adversely affect plant growth and photosynthesis machinery through a disruption of cell organelles, arrangement thylakoid membranes and the electron transport chain. Herein, we probed the effect of drought stress on photosynthetic performance of Chenopodium quinoa Willd. Beforehand, plants were subjected to water deficit (as 15% Field Capacity, FC) for one (D-1W) or two weeks (D-2W), and were then re-watered at 95% FC for 2 weeks. Light and electron microscopy analysis of leaves showed no apparent changes in mesophyll cell organization and chloroplast ultrastructure after one week of drought stress, while a swelling of thylakoids and starch accumulation were observed after the prolonged drought (D-2W). The latter induced a decrease in both PSI and PSII quantum yields which was accompanied by an increase in F0 (minimum fluorescence) and a decline in Fm (maximum fluorescence). Drought stress influenced the fluorescence transients, where the major changes at the OJIP prompt FI level were detected in the OJ and IP phases. Prolonged drought induced a decrease in chl a fluorescence at IP phase which was readjusted and established back after re-watering and even more an increase was observed after 2 weeks of recovery. The maximum quantum yield of primary photochemistry (φPo) was unaffected by the different drought stress regimes. Drought induced an increase in the ABS/RC and DI0/RC ratios which was concurrent to a stable φPo (maximum quantum yield of PSII primary photochemistry). A substantial decrease in PI(ABS) was detected especially, during severe drought stress (D-2W) suggesting a drop in the PSII efficiency and the level of electron transport through the plastoquinone pool (PQ pool) towards oxidized PSI RCs (P700+). The immunoblot analysis of the main PSII proteins revealed considerable changes in the D1, D2, CP47, OEC, PsbQ and LHCII proteins under drought. These changes depend on the stress duration and recovery period. The main message of this investigation is the elevated recovery capacities of PSII and PSI photochemical activities after re-watering.