This study aimed to investigate the combined effect of storage at 4 degrees C (10-days) and in vitro gastrointestinal digestion on the phytochemical profile of red beet (Beta vulgaris) and amaranth (Amaranthus sp.) microgreens. The untargeted profiling based on UHPLC-QTOF metabolomics allowed annotating 316 compounds, comprising mainly polyphenols and lipids. An impact of storage on the total phenolic content (TPC) was observed, with a maximum increase at 10-days of storage for both red beet (+ 1.3-fold) and amaranth (+ 1.1-fold). On the other hand, in vitro digestion of both red beet and amaranth microgreens produced a significant increase in TPC (36-88%), CUPRAC (27-40%), DPPH (6-43%), and BC (41-57%) to reach the maximum at 10 days of storage. Tyrosinase inhibitory potential also decreased following digestion. The combination of biochemical changes occurring in microgreen immature plants (likely in response to the harvest stress) with changes during digestion, determined the actual functional value of microgreens.