Frozen yoghurt is a refreshing and nutritious dessert, with or without the flavour that combines the texture of ice cream and yoghurt. Several previous studies have been conducted on Jerusalem artichoke tubers due to their components, which contain inulin compounds and other nutrients with beneficial properties of fresh yoghurt. However, limited studies explored the potential benefits of the addition of Jerusalem artichoke tuber powder as a fat replacer on the physicochemical properties and survival of probiotics in frozen yoghurt. In this respect, the aim of this study was to determine the effect of Jerusalem artichoke tuber powder (JATP) (0, 5, 10, 15, and 20% w/w) of the fat source used in the mix as a fat, and sugar replacer in frozen yoghurt production. The microbiological, physicochemical, textural, and sensory properties of frozen yoghurt were investigated. Samples with JATP contained viable counts of bifidobacterium bifidum BGN4 and Lactobacillus casei Lc-01 of 7 log cfu/g during 90 days of storage, as compared to the control sample. The highest viability of probiotics was obtained in the sample formulated with 10% JATP. The formulation of frozen yoghurt with JATP increased the acidity and enhanced the overrun. Compared with the control sample, the incorporation of JATP into frozen yoghurt increased the melting resistance, overrun, and viscosity of the frozen yoghurt. The addition of JATP up to 10% significantly increased sensory attributes. Collectively, the study concluded that the enrichment of frozen yoghurt with JATP up to 20% will provide consumers with health benefits and could be introduced to markets as functional frozen yoghurt.