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True regeneration of the pulp-dentine complex is the ultimate goal of regenerative endodontic procedures (REPs). Despite favourable clinical outcomes, such as resolution of apical periodontitis, continued root elongation and apical closure, histological evidence suggests that most clinical cases result in tissue repair rather than true regeneration. This discrepancy arises from the intricate requirements for optimising the microenvironment, which encompasses two essential stages: disinfection and regeneration. These two stages are not necessarily sequential; they can overlap and be highly interconnected, influencing each other. Current REPs protocols have limitations in both disinfection and regeneration. Endodontic biofilms exhibit a notable tolerance to disinfectants and have the capability of recovery, which negatively affects the odontogenic potential of stem cells. Additionally, immune cells, particularly M1 and M2 macrophages, interact with stem cells and affect their regenerative capacity. Standard irrigants and intracanal medicaments often fail to eliminate biofilms, compromising stem cell viability and differentiation potential. On the regeneration side, age-related decline in stem cell function reduces cell survival and differentiation capacity, while insufficient delivery and lack of control over signalling molecules limit odontogenesis, angiogenesis, and neurogenesis. Commonly used scaffolds for REPs lack the structural, biochemical and biological precision required to guide regeneration of well-organised tissue. Furthermore, a microenvironment characterised by hypoxia, restricted nutrients and limited neurovascular ingrowth further constrains regenerative outcomes. This review will focus on the limitations of the current regenerative microenvironment in REPs and discuss emerging strategies aimed at integrating infection control with tissue engineering design. It also highlights the need for novel antimicrobial approaches and advanced tissue engineering strategies in REPs. Multifunctional biomaterials, such as chitosan nanoparticles, antimicrobial peptides and hierarchically structured scaffolds, may ultimately facilitate true biological regeneration of the pulp-dentine complex.