This study introduces a novel functional sugar-free dessert fortified with mahua (Madhuca longifolia (L.) J.F. Macbr.) flowers. Mahua flowers are rich in valuable nutrients that may provide functional status and give added value to traditional desserts. In this research, we modified a traditional dairy kheer dessert by substituting some ingredients with roasted mahua flowers. The research included a control sample (a traditional dessert) and four experimental ones (desserts with 150, 200, 250, and 300 g of mahua flowers). The bioactive profile and metabolomics of the desserts were described using the method of high-resolution mass-spectrometry. The sample with 250 g of mahua flowers had higher organoleptic characteristics compared to the other experimental samples and was selected for further study. This sample demonstrated higher total phenolics, total flavonoids, and DPPH compared to the control dessert. We detected a total of 39 major bioactive metabolites in the dessert with mahua flowers, including rhusflavanone, miquelianin, catechin, quercetin, rutin, robinetinidol 3-O-gallate, eriocitrin, ferulic acid, and kaempferol 3-apioside-7-rhamnosyl-(1- > 6)-(2"-(E)-caffeoyl glactoside). All these substances are associated with numerous health benefits. As mahua flowers have antioxidant, antibacterial, and anti-inflammatory properties, they can be used in commercial production of functional food products.