The skin represents a complex ecosystem where host cells and microbiota coexist in dynamic equilibrium. Disruption of this balance contributes to inflammation and diseases, while natural compounds may help restore it. For centuries, marigold and chamomile have been among the most valued medicinal plants in traditional herbal medicine, widely used for treating wounds, skin inflammation, and irritations. Their long-standing therapeutic reputation is supported by rich phytochemical profiles – triterpenoids, flavonoids, phenolic acids in marigold, and sesquiterpene lactones, flavonoids, and coumarins in chamomile – known to exert anti-inflammatory, antioxidant, and soothing effects. In this study, Calendula officinalis and Matricaria recutita flower extracts’ effects were investigated on human skin microbiota and dermal cells. Both extracts remained chemically stable under microbial exposure and did not generate new metabolites, highlighting resistance to microbial metabolism. Neither extract disrupted community structure; instead, they selectively modulated microbial taxa, decreasing potentially pro-inflammatory families (Staphylococcaceae, Corynebacteriaceae, and Enterococcaceae) and enriching the Bacillales and Bacillaceae families. On the cellular level, at ≤250 µg/mL, both extracts were biocompatible with fibroblasts and keratinocytes. Marigold flower extract showed no significant anti-inflammatory effect in keratinocytes, as IL-6 and IL-8 secretion remained comparable to the stimulated control. In contrast, Chamomile flower extract markedly reduced IL-6 levels in a dose-dependent manner, with moderate effects on IL-8. In fibroblasts, both extracts had strong suppression of IL-6 and IL-8 at higher concentrations. These findings reveal a dual mechanism – direct cellular modulation and indirect microbiota-mediated rebalancing-supporting the traditional therapeutic efficacy of C. officinalis and M. recutita in skin health.