The objective of this research was to test the influence of various natural substances on acid production, growth, and viability of characteristic microorganisms in yogurt and probiotic fermented dairy foods. Oligofructose, inulin, honey, and the dried biomass of Spirulina (Arthrospira) platensis were found to stimulate the growth rate and acid production activity of the major thermophilic diary cultures tested and, in addition to this, the presence of the aforementioned substrates also improved the survival of starter bacteria in fermented milk products during storage. The reduced production time of cultured milks resulted in increased production efficiency. The stimulatory and/or protective effect of oligofructose, inulin, honey, and Spirulina on Bifidobacterium spp. is probably the most important finding of this study because bifidobacteria do not grow well in milk and they have low survival rates in conventional fermented milks. Some of the bioactive substances tested were also capable of exerting an antifungal effect on spoilage yeasts and molds, and improving the nutritional and sensory properties of the final product, thus providing a new opportunity for manufacture of functional fermented dairy foods.