The mitochondrial respiratory chain in various protists, many fungi and all plants consists of the ATP-coupling cyanide-sensitive cytochrome pathway and the cyanide-resistant alternative non-phosphorylating electron transport pathway. The alternative pathway reduces O2 to H2 O, and this is mediated by a terminal alternative oxidase (AOX). The unicellular green alga Chlamydomonas reinhardtii reacts to phosphorus (P) limitation conditions with the induced expression of many genes among which only one, AOX1, encodes mitochondrial protein. In this study, we demonstrated a sharp increase in AOX1 protein abundance and AOX capacity under P deprivation. Our data revealed that PSR1 transcription factor is not the only regulator of AOX1 during P deprivation. Using biochemical and molecular-genetic approaches, we showed that AOX1 is tuned at transcriptional and post-transcriptional levels, and nitric oxide is an integral part of this regulation. The previously unidentified links between AOX1 synthesis and its capacity, and the truncated hemoglobin 2 (THB2)-dependent pathway could unveil the mechanism by which the alternative respiratory pathway is integrated into the acclimation of cells to stress conditions.