Natural preservatives such as garlic and ginger can be added to the formulation of fresh fruit juices to encourage the consumption of health-promoting foods. In this study, the influence of garlic and ginger and the storage conditions on physicochemical and microbiological characteristics of fruit juices were investigated. The fruit juice assortments were produced from apple, apple and pumpkin, and apple and pomegranate and were treated with 0.5 g garlic powder, 0.5 g ginger powder, and 0.25 g mix of garlic and ginger powders. A total of 12 unpasteurized samples were produced, of which 3 were control samples. Samples stored at 20 and 4 °C were analyzed at 0, 3, 6, and 9 days for water activity (aw), pH, titratable acidity (TA), total soluble solids (TSS), electrical conductivity (EC), vitamin C, color parameters, total number of germs, yeasts, and molds, Listeria, Enterobacteriaceae, and Escherichia coli. Results showed that aw, pH, TSS, and vitamin C content decreased during storage of fruit juice samples, while TA increased. The lowest increase in total number of aerobic mesophilic germs was determined for the apple and pumpkin juice with garlic and ginger and apple juice with garlic.