Increases in soil salinity impact growth and agricultural yield by inhibiting plant functions. Interactions of fungal endophytes with crop plants can improve tolerance and is a less expensive approach. Here, the role of Trichoderma harzianum T-22 in alleviating NaCl-induced stress in two barley genotypes (cv. Vlamingh and cv. Gairdner) has been investigated. Metabolomics using GC-MS for polar metabolites and LC-MS for lipids was employed to provide insights into the biochemical changes in inoculated roots during the early stages of interaction. T. harzianum improved root growth of both genotypes in saline conditions whereas uninoculated roots were significantly shorter after salt treatment. The fungus reduced relative concentration of sugars in both genotypes under saline conditions but there was no change in organic acids. Amino acids decreased only in cv. Gairdner in fungus-inoculated roots under saline conditions. Lipid analysis suggested that salt stress causes large changes in roots but that inoculation with fungus greatly reduces the extent of these changes. By studying a tolerant and a sensitive genotype and their responses to salt and inoculation we have been able to develop hypotheses that explain the tolerance of Vlamingh to salt and how fungal inoculation changes the response of Gairdner to improve its tolerance.