Skin aging is a multidimensional biological process driven by intrinsic chronological changes, exposomal stress, endocrine–metabolic shifts, extracellular matrix remodeling, inflammaging, oxidative injury, barrier impairment, and microbiome dysbiosis. This review integrates current evidence on the endocrine–microbiome–skin axis and evaluates microbiome-directed bioactive strategies for preserving cutaneous homeostasis during aging. Particular attention is given to probiotics, prebiotics, postbiotics, synbiotics, phytoestrogens, polyphenols, bioactive peptides, antioxidants, mitochondrial protectors, adaptogens, and metabolic modulators. Their mechanisms are discussed in relation to collagen homeostasis, mitochondrial function, lipid barrier integrity, immune regulation, microbial metabolite signaling, and systemic endocrine–metabolic status. The review also examines advanced delivery platforms, including liposomes, solid lipid nanoparticles, nanostructured lipid carriers, polymeric nanocarriers, nanoemulsions, encapsulated microbiome-active systems, and stimuli-responsive carriers, emphasizing their potential to improve compound stability, skin retention, controlled release, and target-site precision. Translational limitations are critically addressed, including strain and formulation specificity, insufficient long-term safety data, incomplete nanocarrier toxicology, regulatory ambiguity, and the need for personalization according to hormonal, metabolic, and microbiome profiles. Overall, microbiome-directed bioactive compounds combined with precision delivery systems represent a promising, but still evolving, strategy for delaying skin aging and restoring cutaneous homeostasis.