Phytoestrogens, polyphenolic secondary metabolites prevalent in many plant-based feed ingredients, are increasingly incorporated into aquafeeds due to the shift away from fishmeal. These phytochemicals play an important role in plant growth, development, and maintenance. However, phytoestrogens may act as xenoestrogens by mimicking the actions of endogenous steroidal oestrogens in animals, interfering with the natural functions of oestrogens and adversely affecting host metabolism. In aquafeed, they may show several adverse effects on the host, particularly related to reproduction and sex differentiation of fish. This review outlines the classification and sources of phytoestrogens, evaluates their impact on fish health, particularly focusing on endocrine disruption and feminization, and the strategies to reduce phytoestrogen content in plant-based feed ingredients. The adverse effects of phytoestrogens on fish growth, reproduction, and sex differentiation are also explored. Additionally, the review highlights the need to focus on species-specific responses, broader ecological implications, and regulatory perspectives to provide a comprehensive understanding of phytoestrogens in aquaculture.