Persistent Organic Pollutants (POPs), including polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), and polybrominated diphenyl ethers (PBDEs), are widespread environmental contaminants known to bioaccumulate in marine organisms. On São Tomé Island, where five of the seven sea turtle species occur, green turtles (Chelonia mydas) are known to nest regularly. This study assessed POP levels (PCBs, OCPs, and PBDEs) in nesting females and in their eggs to evaluate maternal transference and explore associations with egg morphology, composition, and quality, as well as reproductive success (e.g., hatching rate and emergence rate). Blood samples from nesting females and yolk samples from their freshly laid eggs were analysed, with POPs detected in both, confirming maternal transfer. Transfer rates varied across compounds, influenced by lipophilicity and specific congener properties, indicating distinct transfer efficiencies and pathways. ΣPCBs showed the highest concentrations, followed by ΣOCPs and ΣPBDEs. The yolk of sea turtle eggs, rich in lipids, is the primary energy and nutrient source for developing embryos. Fatty acids (FAs)—the functional components of these lipids—play key roles in membrane structure, metabolism, and embryonic growth. POPs detected in maternal blood were associated with changes in yolk FA profiles, especially within the polar lipid fraction, crucial for metabolic and structural functions. OCPs in maternal blood strongly influenced phospholipid-associated FAs in the yolk, potentially affecting key processes like phospholipid synthesis and eicosanoid production. Maternal blood PCBs levels were associated with reduced egg diameter and yolk weight. Additionally, PBDE-47 levels in egg yolks were linked to lower hatching success, suggesting that contaminant-driven disruption of lipid metabolism may impair embryonic development. This study provides novel data on POP contamination in green turtles from São Tomé, highlighting how maternal exposure can influence egg quality and reproductive output. The findings emphasise the need for continued monitoring and informed conservation strategies for the endangered species.