Solid-state fermentation of cereals with edible fungi is a promising strategy for producing functional flours. Hypothetically, the nutritional and functional properties of these flours could be modulated by manipulating substrate composition, fungal species, and incubation conditions. This article reports the variation over time in nutritional, polyphenol, and triterpene contents, as well as the antioxidant activity of rice and wheat fermented with <i>Ganoderma sessile</i> and <i>Pleurotus ostreatus</i>. Solid-state fermentation significantly improved the antioxidant power of the substrates which seemed to be highly correlated with the increase of the phenolic compounds. This increase peaked in the second to third week and decreased after this point. Triterpene content also increased, especially in substrates fermented with <i>G. sessile</i>. Substrates fermented with <i>G. sessile</i> showed higher values than those fermented with <i>P. ostreatus</i> in all compounds, which could be a result of a higher growth rate. Fermented wheat showed higher values than fermented rice in all measured compounds except reducing sugars which can be related to a slower progress in the fermentation due to the more complex structure of the wheat grain. Our results reinforce the importance of substrate and strain selection for product modulation to meet the industry's growing needs.