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Beyond their conventional role as passive transdermal delivery vehicles, microneedle (MN) platforms now function as active bio-interfaces capable of modulating therapeutic responses in both localized and systemic diseases. This review summarizes recent advances in MN technology, focusing on the transition from traditional matrix-controlled delivery to bioactive microneedles. Although localized applications at barrier surfaces, such as treating cutaneous disorders and mucosal lesions, remain a fundamental focus, this review emphasizes the application of MNs in complex chronic metabolic diseases (e.g., diabetes), oncology (e.g., melanoma and glioblastoma), and deep-tissue degenerative diseases of the cardiovascular, nervous, and musculoskeletal systems. Integrating stimuli-responsive materials, including metal-organic frameworks (MOFs), aggregation-induced emission luminogens (AIEgens), and smart hydrogels, with external physical stimuli enables autonomous, closed-loop interventions, thereby advancing personalized systemic therapy. Furthermore, we summarize recent progress in applying MNs to non-traditional sites and deep-tissue repair. Finally, rather than focusing solely on phenotypic efficacy, we discuss key translational challenges, including manufacturing scalability, biosafety, and regulatory pathways, to guide future clinical translation.