An increasing number of oscillating or fluctuating cellular systems have been recently described following the adaptation of fluorescent technology. In diverse organisms, these variously involve signalling factors, heat production, central metabolism and reactive oxygen species (ROS). In response to many plant stresses and primarily via the influence of ROS, changes in mRNA and protein levels or in vivo activity of alternative oxidase are often observed. However, in several investigations, a lack of correlation between the mRNA, protein and in vivo activity has been evident. This discrepancy has made it questionable whether the induction of alternative oxidase has importance in regulating alternative pathway activity in vivo, or being diagnostic for a role of alternative oxidase in stress tolerance and ROS avoidance. Here, we suggest a role of alternative oxidase in counteracting deleterious short-term metabolic fluctuations, especially under stress conditions. This model emphasizes the importance of peak activity for establishing protein levels and allows an amalgamation of the present status of physiological, cellular and molecular knowledge.