The combination of multiple strains and multiple species in lactic acid bacteria-based fermented milk offers the potential for nutritional and sensory attributes, making it an attractive option for developing high-quality and health-promoting probiotic yoghurt-like fermented milk products. In the present study, four combinations of yoghurt-like fermented milk samples: Sample 1 (Control), Sample 2 (Lactobacillus desidiosus), Sample 3 (Lactobacillus fermentum), and Sample 4 (Lactobacillus desidiosus and Lactobacillus fermentum) were developed. Proximate composition (moisture, ash, protein, fat, carbohydrate), physicochemical (pH, titratable acidity, syneresis, total soluble sloid), microbiological (Lactobacillus bacteria, yeast and mold, and coliform bacteria), and sensory properties (color, flavor, texture, taste, and overall acceptability) were assessed under refrigerator conditions (4 °C) from 0 to 28 days of storage period. Proximate composition differed significantly (p < 0.05) among samples for moisture (49.34–79.32%), ash (1.14–0.31%), protein (3.72–3.21%), fat (11.23–5.62%), and carbohydrate (33.11–12.98%). Yoghurt-like fermented milk containing Lactobacillus desidiosus as single or in combination with Lactobacillus fermentum resulted in reduced pH levels (6.02–3.49), total soluble solid (41.66–24.66%) and increased syneresis (30.04–65.52%), titratable acidity content (0.42–1.62%). Single or combination of Lactobacillus desidiosus and Lactobacillus fermentum significantly (p < 0.05) reduced Lactobacillus bacteria (8.17–6.01 Log CFU/g), yeast, and mold (1.45–1.19 Log CFU/g). Additionally, none of the samples of probiotic yoghurt-like fermented milk showed any detectable coliform count, indicating the possibility of prolonging the shelf life. The sample prepared by Lactobacillus desidiosus had the highest sensory ranking (8.10) at day 0 and during storage than other samples. In conclusion, the inclusion of Lactobacillus desidiosus and Lactobacillus fermentum strains in the composition of production starter cultures holds great promise. The utilization of these enriched starter cultures enables the production of healthy food products that maintain their quality throughout the entire storage period.