PurposeCrops are increasingly affected by drought; hence, the current study explored the potential role of three desert endophytic fungi, Aspergillus fumigatus, Aspergillus terreus and Talaromyces variabilis, in conferring drought tolerance in tomato plants.Design/methodology/approachPreserved endophytic fungi from a Rhazya stricta desert plant were adopted to obtain the required fungal treatment; tomatoes received fungal treatments directly in plastic trays and subsequently in pots. Drought was applied using 15% of PEG-6000 at two stages: flowering and fruiting. The following parameters were measured: pollen sterility, growth characteristics, morphological analysis and biochemical analysis, including proline, gibberellic acid (GA3) and chlorophyll measurements; thus, the data were analyzed statistically using SPSS software.FindingsAll applied endophytes significantly promoted pollen viability and tomato yield under stressed and nonstressed conditions. Interestingly, these endophytes significantly enhanced the number of trichomes under drought stress and promoted tomato fruit quality. The colonized tomato plants accumulated a high proline level under drought stress but lower than un-inoculated stressed plants. Also, a significant rise in growth characteristics was observed by A. fumigatus and A. terreus under normal conditions. Moreover, both raised GA3 levels under drought-stressed and nonstressed conditions. Also these two endophytes enhanced chlorophyll and carotenoid contents under drought stress. Fruit characteristics were enhanced by nonstressed T. variabilis and stressed A. fumigatus.Originality/valueThe present endophytic fungi provide impressive benefits to their host in normal and drought-stressed conditions. Consequently, they represent valuable sources as sustainable and environmentally friendly alternatives to mitigate drought stress.