Oxidative stress in plants and green algae has multiple damaging effects, and leads to the degradation of Ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco). We recently showed for the green algae Chlamydomonas reinhardtii that in response to a photo-oxidative stress, nascent synthesis of its chloroplast encoded large subunit (LSU) stops. In parallel, newly synthesized small subunits (SSU) that are encoded by the nucleus are rapidly degraded, thus assembly of new holoenzyme particles is inhibited. Here we show that under extreme oxidizing conditions, the steady-state level of the SSU is also reduced. Cleavage of the LSU under oxidizing conditions is well established, and we show, using sucrose gradients, that the resulting fragments of the LSU co-exist as parts of the holoenzyme. In parallel, we demonstrate the selective in-vivo formation of high-density aggregates of Rubisco particles, in response to oxidative stress. Given the known tendency of unassembled LSUs to aggregate, we propose that the rapid elimination of the SSU during oxidative stress along with the fragmentation of the LSU and formation of intra-protein disulfide bridges, leads to the observed aggregation of Rubisco particles. Indeed, we note here a substantially decreased ratio of SSU in the aggregated Rubisco particles. We also observed that this aggregation marks the viability threshold of C. reinhardtii cells exposed to oxidative stress.