The oceans’ biological pump (BP) exports large amounts of particulate organic carbon (POC) to the mesopelagic zone (base of the euphotic zone – 1000 m depth). The efficiency at which POC is transferred through the mesopelagic zone determines the size of the deep ocean carbon store. Few observational BP studies focus on the mesopelagic, often leading to the need to oversimplify the representation of processes within this depth horizon in numerical models. In this review, we identify and describe three interlinked biological processes that act to regulate and control the transfer efficiency of POC through the mesopelagic zone; (1) direct sinking of phytoplankton cells and aggregates, (2) zooplankton community structure and (3) the microbial loop and associated carbon pump. We reveal previously unidentified relationships between planktonic community structure and POC transfer efficiency for specific regions. We also compare mesopelagic POC remineralisation depth (a proxy for POC transfer efficiency) with the permanent thermocline in different regions. Our analysis shows that even when mesopelagic POC transfer efficiency is low, such a transfer efficiency does not necessarily mean low carbon sequestration if the permanent thermocline is shallow, and we define a carbon sequestration ratio (C_seq, the remineralisation depth divided by the permanent thermocline) to highlight this. Low latitude regions typically have a higher C_seq than temperate and polar regions, and thus could be more important in transferring carbon on long timescales than previously thought. POC transfer efficiency should be regularly discussed in the context of the physical water properties such as the permanent thermocline, to truly assess an oceanic region’s ability to sequester carbon. Improved understanding of mesopelagic ecological processes and links to surface processes will better constrain ecosystem models and improve projections of the future global carbon cycle.