The mid-Piacenzian Warm Period (mPWP; ~3.264&ndash;3.025 Ma) marks the most recent episode of sustained global warmth, characterised by atmospheric carbon dioxide (<em>p</em>CO₂) levels similar to those of today. Despite this, our understanding of the vertical structure of the Pliocene ocean and its role in modulating global carbon cycling during this period remains poorly resolved. Here, we combine planktic (coccolith and planktic foraminifera) and benthic (benthic foraminifera) stable carbon (&delta;¹³C) and oxygen (&delta;¹⁸O) isotope records from the International Ocean Discovery Program (IODP) Site U1476 in the western tropical Indian Ocean (Mozambique Channel), to reconstruct surface-to-deep ocean conditions during the mPWP. The consistently high vertical &delta;¹³C and &delta;¹⁸O gradients indicate long-term thermal stratification and increased carbon export in this moderately elevated <em>p</em>CO₂ world. Distinct isotopic signatures observed between the deep-photic zone coccolithophore <em>Florisphaera profunda </em>which dominates the coccolith assemblages, and mid-photic zone planktic foraminifera <em>Globigerinoides ruber</em> suggest ecological partitioning and differing sensitivities to upper ocean dynamics (e.g., stratification, nutrient supply, light intensity). A transient breakdown in stratification and deep ocean carbon storage during Marine Isotope Stage M2 (~3.30&ndash;3.28 Ma), a glacial interval preceding the peak warmth of the mPWP, demonstrates the vulnerability of the tropical ocean structure to high-latitude climate forcing. Spectral analysis reveals pronounced obliquity-paced variations in both &delta;¹³C and &delta;¹⁸O records, linking high-latitude orbital forcing to carbon cycling in low-latitude regions. These findings offer important new constraints on the ocean&ndash;atmosphere carbon feedback during the mPWP and underscore the previously underappreciated role of the tropical Indian Ocean as a dynamic component of global carbon cycling during past warm periods.