New eating habits and diversification of tastes of consumers have led to the scientific community and the food industry to expand the range of probiotic foods and novel probiotic ingredients. Scant information is available about the viability and functionality of probiotics during shelf life and its effect on the nutritional characteristics of dairy-free products. The aim of the study was to formulate a fermented dairy-free dessert using a novel food ingredient based on a pumpkin by-product and containing Lactobacillus casei (ATCC®393™) (NFI). The effect of NFI and the soluble solids (SS) of soy milk on the probiotic viability, physical stability, colour, and firmness of dairy-free dessert was studied using a response surface methodology. The different levels of SS and NFI significantly (p < 0.05) affected the response variables. Thereafter, two formulations were selected and the physico-chemical, nutritional and organoleptic characterization were evaluated. The L. casei count reached the desired therapeutic level (>10⁷ UFC mL⁻¹) after gastrointestinal digestion at 21 days of storage. In general, both the fermentation process and storage reduced (p < 0.05) the content of phytic acid, raffinose and stachyose, which implies a nutritional improvement of the final product. Scores above 5.0 on a 9-point scale were obtained for colour, odour, texture and overall acceptability in the consumer acceptance test. Therefore, a dairy-free dessert with good physical properties, suitable nutritional characteristics, and sensorial acceptability could be successfully formulated with the NFI.