Kefir-based fermentation products exhibit antioxidant and anti-inflammatory effects against oxidative stress, inflammation, platelet activation and aggregation, and other related manifestations, thereby preventing the onset and development of several chronic diseases. Specifically, water kefir, a symbiotic culture of various microorganisms used for the production of several bio-functional fermented products, has been proposed for its health-promoting properties. Thus, water kefir grains and its apple pomace-based fermentation beverage were studied for bioactive amphiphilic and lipophilic lipid compounds with antioxidant, antithrombotic, and anti-inflammatory properties. Total lipids (TL) were extracted and further separated into their total amphiphilic (TAC) and total lipophilic content (TLC), in which the total phenolic and carotenoid contents (TPC and TCC, respectively) and the fatty acid content of the polar lipids (PL) were quantified, while the antioxidant activity of both TAC and TLC were assessed in vitro, by the ABTS, DPPH, and FRAP bioassays, along with the anti-inflammatory and antithrombotic activity of TAC against human platelet aggregation induced by the thrombo-inflammatory mediator, platelet-activating factor (PAF) or standard platelet agonists like ADP.ATR-FTIR spectra facilitated the detection of specific structural, functional groups of phenolic, flavonoid, and carotenoid antioxidants, while LC-MS analysis revealed the presence of specific anti-inflammatory and antithrombotic PL bioactives bearing unsaturated fatty acids in their structures, with favorable omega-6 (-6)/omega-3 (-3)polyunsaturated fatty acids (PUFA), which further support the findings that the most potent antioxidant, anti-inflammatory and antithrombotic bioactivities were observed in the TAC extracts, in both water kefir grains and beverage cases. The detection of such bioactive components in both the uncultured water kefir grains and in the cultured beverage further supports the contribution of water kefir microorganisms to the bioactivity and the bio-functionality of the final fermented product. Nevertheless, the extracts of the beverage showed much stronger antioxidant, anti-inflammatory, and antithrombotic activities, which further suggests that during the culture process for producing this beverage, not only was the presence of bioactive compounds produced by kefir microflora present, but biochemical alterations during fermentation of bioactive components derived from apple pomace also seemed to have taken place, contributing to the higher bio-functionality observed in the apple pomace-water kefir-based beverage, even when compared to the unfermented apple pomace. The overall findings support further studies on the use of water kefir and/or apple pomace as viable sources of antioxidant, anti-inflammatory, and antithrombotic amphiphilic bioactive compounds for the production of novel health-promoting bio-functional fermented products.