Piriformospora indica is an endophytic fungus with plant-promoting properties in a wide range of host plants. This study aimed to assess and compare the effects of different P. indica inoculants through morphological and physiological analysis at different times (4, 8, and 12 weeks) after inoculation. The study was conducted in a completely randomized design with three levels of fungus inoculation (non-inoculated, inoculated with P. indica spore and mycelium). The results showed that both P. indica inoculants have a positive effect on measured traits at different times after inoculation. Root and shoot dry weight were increased significantly at 4, 8, and 12 weeks after inoculation. P. indica improved the reproductive phase of tomato resulting in increased dry weight of fruits by up to 51%. Most importantly, the endophyte enhanced tomato fruit yield by up to 73%. Based on experiment data, P. indica increased total chlorophyll (25%), protein (143%), and carbohydrate (44%) content in inoculated plants compared to non-inoculated plants. Besides, P. indica promoted the antioxidant capacity of inoculated plants by increasing CAT and APX activity. In our study, plant inoculation with P. indica also remarkably led to an increase in K (172%) and P (41%) content. Our data showed that both P. indica spore and mycelium have a long-term effect on tomato growth. The application of fungus inoculants promotes plant growth and yield. Hence, P. indica represents a suitable plant-stimulating biofertilizer for tomato in sustainable agriculture. Manuscript profile