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The rationale of the current dissertation research is to investigate health beneficial components and properties of blackberry, broccoli, carrot, cucumber, and milk thistle seed flours. This can lead to potential utilization of these seed flours in nutraceuticals and functional foods. Also, this can add value to oil manufacturers and the seed producers while reducing environmental contaminations. Blackberry, broccoli, carrot, cucumber, and milk thistle seed flours were extracted with 50% acetone and evaluated for their phytochemical compositions along with their potential gut microbiota modulating, free radical scavenging, and anti-inflammatory and anti-proliferative capacities. Thirteen, nine, ten, and fifteen compounds were detected in the blackberry, broccoli, carrot, and milk thistle seed flour extracts, with sanguiin H6, glucoraphanin, kaempferol-3-O-rutinoside, and silychristin as the primary component of each, respectively. All five seed flour extracts enhanced total number of gut bacteria and altered the abundance of specific bacterial phylum or genus in vitro. The blackberry seed flour extract had the greatest relative DPPH radical scavenging capacity and ABTS•+ scavenging capacity values of 362 and 267 μmol trolox equivalent (TE)/g, respectively. Milk thistle seed flour had the greatest oxygen radical absorbing capacity and hydroxyl radical (HO•) scavenging capacity values of 634 and 10420 μmol trolox equivalent (TE)/g, respectively. Also, all five seed flour extracts suppressed LPS induced IL-1β mRNA expressions in J774A.1 cells and the proliferation of LNCaP prostate cancer cell line. The results might be used to promote the value-added food utilization of these seed flours in improving human health.