This study aimed to offer an alternative way for delivering the benefits of the mandarin fruit juice to consumers via spray drying microencapsulation. Two mandarin cultivars, Afourer (A) and Richard Special (RS), were studied. Three types of juice sample were prepared, i.e., the whole fruit juice (A3 & RS3), the flavedo-removed fruit juice (A2 & RS2), and the peel-removed fruit juice (A1 & RS1) samples. Gum Acacia and maltodextrin (ratio of 1:1, w/w) were chosen as wall matrices for aiding the drying of the juice samples while using a microfluidic-jet spray dryer. The properties of the fruit powder (colour, water activity, bulk/trapped density, solubility, hygroscopicity, morphology) and the retention of major phytochemicals (i.e., phenolic and volatile compounds) were examined. The results showed that the powders produced from the whole fruit juices (A3 and RS3) gave higher yellow colour with a regular winkled surface than other powders (A1 & RS1, and A2 & RS2). The water activity of mandarin powders was in a range of 0.14 to 0.25, and the solubility was around 74% with no significant difference among all of the powders. The whole fruit powders had a significantly higher concentration of phenolic compounds (A3, 1023 µg/100 mg vs. A2, 809 µg/100 mg vs. A1, 653 µg/100 mg) and aroma compounds (A3, 775,558 µg/L vs. A2, 125,617 µg/L vs. A1, 12,590 µg/L). This study contributed to the delivery of phenolic and flavour compounds of the mandarin fruits, at the same time minimising waste generation during processing. It also gave insight into the production of spray-dried powders from the whole mandarin fruits.