Calcium (Ca2+) is involved in different cellular functions and signaling pathways, mediating between extracellular and intracellular signals. MAMs (Endoplasmic reticulum-mitochondria associated membranes) are specific close appositions formed by the physical interaction of the ER and the mitochondria, thus regulating the main intracellular Ca2+ flux by means of the communication between the two compartments. This is fundamental to maintain cell function and so it has been proposed as a common mechanism in neurodegeneration. Friedreich's Ataxia (FRDA) is an autosomal recessive neurodegenerative disorder in which patients show reduced levels of frataxin (FXN), a protein fundamentally associated with the mitochondrial matrix. This implies several alterations in signaling pathways related to mitochondrial function. Among these, evidence for dysfunction of intracellular Ca2+ homeostasis has been observed, but the mechanisms involved are unknown. On the other hand, the existence of extra-mitochondrial FXN isoforms highlights the importance of the functional characterization of FXN linked to its subcellular localization and tissue distribution in FRDA. Therefore, the aim of the present work is to determine the involvement of MAMs in the pathophysiology of FRDA, as well as their relevance as potential therapeutic targets of the disease. The study of FXN subcellular localization revealed that FXN is located in MAMs domain, interacting with two of the main proteins responsible for ER-mitochondria Ca2+ exchange. Moreover, FXN deficiency decreases MAMs communication in our cell model both structurally and functionally, decreasing Ca2+ transfer from the ER to the mitochondria. Treatment with Trolox, NAC and compounds targeting MAMs such as Omaveloxolone, Fluvoxamine and Kaempferol, succeeded in rescuing some of the deficiencies observed in the model, highlighting the importance of this domain as a therapeutic target for FRDA. We optimized the Split-TurboID technique to study the interactome of FXN I and II in both the ER/cytosol and the mitochondrial matrix with the aim of elucidating which isoform of FXN might be involved in the regulation of MAMs domain. Results showed that both FXN I and FXN II localize extramitochondrially, interacting with the ER from the cytosol, while FXN I localizes to the mitochondria, exhibiting a dual subcellular localization. Dataset analysis of both interactomes in the ER revealed proteins belonging to MAMs, with some involved in Ca2+ homeostasis suggesting that both are present in this domain and would be implicated in intracellular Ca2+ homeostasis. In short, our results point to a clear involvement of FXN in the regulation of the MAMs domain, which may contribute to the pathophysiology of FRDA. However, the contribution of each isoform in these processes needs to be clarified. Taken together, our findings open a field of possibilities focused on the communication of MAMs as a possible therapeutic strategy for FRDA.