The use of intact photosynthetic organisms (e.g. microalgae or cyanobacteria) for biotechnological approaches is a promising avenue to extract sustainable energy from oxygenic photosynthesis. More particularly, exogenous quinones can act as electron shuttles to reroute part of the photosynthetic electron flow of living cells to an outer collecting electrode. This encouraging approach is however hampered by reported poisoning or side-effects of exogenous quinones on the cell bioenergetics. In order to contribute to understand those effects, we investigated the modes and sites of interaction of two model quinones (2,6-DCBQ and 2,6-DMBQ) with the respiratory and photosynthetic electron transfer chains of the green alga Chlamydomonas reinhardtii. By considering different analytical tools (chlorophyll a fluorescence, transient absorption spectrometry, O2 consumption rate), the two exogenous quinones are shown to hamper the photosynthetic electron transfer from photosystem II (PSII) to the cytochrome b6f and, at longer term, PSII damage. In addition, the investigated quinones initiate the suppression of mitochondrial respiration, illustrated by the decrease of O2 consumption. This results in the diminution of the ATP exchanges between mitochondrion and chloroplast responsible for the generation of the proton motive force across the thylakoid in darkness, and in turn affects the performances of the CF1FO ATPase. For all those effects, 2,6-DCBQ was more effective than 2,6-DMBQ in agreement with its higher redox potential and partition coefficient values. This work provides a new framework for the study of biophotovoltaic devices using photosynthetic organisms and quinones as mediators and could be extended to find the best candidates combining efficient bioelectricity production and limited toxicity.