Within the present study, the effects of fermentation on the anti-inflammatory and anti-platelet properties of both homemade and commercially purchased bovine dairy and almond, coconut, and rice-based dairy alternatives were evaluated. The extracted total lipids (TL) from homemade and commercially purchased fermented and unfermented bovine, almond, coconut, and rice-based products were further separated into their neutral lipids (NL) and polar lipids (PL) fractions by counter current distribution. The TL, PL, and NL of each sample were assessed in human platelets against the inflammatory and thrombotic mediator, platelet-activating factor (PAF), and the well-established platelet agonist, adenosine 5′ diphosphate (ADP). In all samples, the PL fractions showed significantly stronger inhibitory effects against human platelet aggregation induced by PAF or ADP, in comparison to the TL and NL, with higher specificity against PAF. PL of all fermented products (bovine yogurt and fermented dairy alternatives from almond, rice, and coconut), exhibited the strongest anti-inflammatory and anti-platelet potency, in comparison to PL from their initial pasteurized materials (bovine milk and rice, almond, and coconut-based dairy alternative drinks). PL of the pasteurized rice-based drink and, especially PL from the novel homemade rice-based fermented product (HMFRD), showed the strongest anti-PAF and anti-ADP potency compared to all samples, with anti-PAF activity being most potent overall. The unfermented pasteurized coconut-based drink showed the lowest anti-inflammatory and anti-platelet potency, and the bovine and almond-based fermented products showed an intermediate effect. Further lipidomics with LC-MS analysis of all these PL fractions revealed that fermentation altered their fatty acid content in a way that decreased their degree of saturation and increased the content of unsaturated fatty acids, thus providing a rationale for the stronger anti-inflammatory and anti-platelet potency of the more unsaturated PL fractions of the fermented products. This study has shown that fermentation alters the fatty acid content and the bio-functionality of the PL bioactives in both fermented bovine dairy and plant-based dairy alternatives, and subsequently improved their anti-inflammatory and anti-platelet functional properties.