Plant cells suffer alterations of their redox state and increase mitochondrial ROS generation during salinity. To avoid this, they activate several mitochondrial antioxidant and redox systems including the alternative oxidase (AOX), superoxide dismutase (SOD) and the ascorbate-glutathione (ASC-GSH) cycle components in a coordinated manner. The redox-sensitive mitochondrial thioredoxin (Trx) system may be responsible for this coordination through the redox regulation of target proteins. On top of this, metabolic perturbations induced by salinity may lead to alterations of the redox state of the Trx system. In order to explore the association between redox and metabolic changes occurring in mitochondria under saline conditions, we analyzed the salt-stress responses of mitochondrial antioxidant systems and metabolism in wild type (WT) and two knock-out (KO) AtTrxo1 lines. The activities of Mn-SOD and components of the ASC-GSH cycle were determined in isolated mitochondria, together with an evaluation of the AOX redox state, the oxidative stress, and catalase activity. Moreover, the in vivo activities of cytochrome (COX) and alternative mitochondrial respiratory pathways and primary metabolites profile were determined. Our results show that the lack of Trxo1 neither resulted in oxidative stress at the mitochondrial level nor in an upregulation of the antioxidant enzymes under salinity, although glutathione reductase (GR) maintained its high constitutive level as observed in control conditions. Moreover, the AOX was found invariably in its reduced monomeric state and displayed a reduction of its in vivo activity in all genotypes after the salt treatment, probably due to the mild severity of the treatment. Interestingly, trxo1 mutants displayed altered patterns in AOX isoforms and in the activities of the ASC-GSH cycle components and the electron partitioning to the AOX pathway indicating a reorganization of the different antioxidant systems. Furthermore, decreases on glucose and fructose levels in both trxo1 mutants coincided with an increased respiration through the COX pathway under control conditions. All these changes collaborate to maintain a low oxidative stress and the energy demand in both, control and salinity conditions and reflect the acclimation of all the genotypes to the applied stress.