The following article describes new research about the design, construction and installation of the new prototype of a vacuum dryer with an ejector system. Moreover, the testing of this new prototype involved comparing the qualities of fruit dried in a vacuum drier with an ejector system to fruit dried in a convectional vacuum drier. The data obtained were then analyzed and presented. Due to their economic relevance and highly valuable nutritional value and sensory properties, sour cherries and apricots have been chosen to be the subjects for the testing. The most appropriate quality indicators for analyzing were moisture content, aw value, share and penetration force, total phenol, flavonoid and anthocyanin content and antioxidant activity (FRAP, DPPH and ABTS test). The main results of this study were achieved by designing, constructing, installing and testing the usage of the innovative prototype of a vacuum dryer with an ejector system in the laboratory of the Technology of fruit and vegetable products of the Faculty of Technology Novi Sad, University of Novi Sad. Based on our analyses of the obtained data, it was concluded that vacuum dryer with an ejector system are similar to vacuum dryer with a vacuum pump in terms of all tested physical, chemical and biological properties of dried samples. We observed similarities in some of the most important parameters, including product safety and quality, such as the aw value and the total phenol content, respectively. For example, in dried sour cherry, the aw values ranged from 0.250 to 0.521 with the vacuum pump and from 0.232 to 0.417 with the ejector system; the total phenol content ranged from 2322 to 2765 mg GAE/100 g DW with the vacuum pump and from 2327 to 2617 mg GAE/100 g DW with the ejector system. In dried apricot, the aw ranged from 0.176 to 0.405 with the vacuum pump and from 0.166 to 0.313 with the ejector system; total phenol content ranged from 392 to 439 mg GAE/100 g DW with the vacuum pump and from 378 to 428 mg GAE/100 g DW with the ejector system.