Given the vital role of thyroid hormones (THs) in vertebrate development, it is essential to identify chemicals that interfere with the TH system. Whereas, among non‐mammalian laboratory animals, fish are the most frequently utilized test species in endocrine disruptor research, e.g. in guidelines for the detection of effects on the sex hormone system, there is no test guideline (TG) using fish as models for thyroid‐related effects; rather, amphibians are being used. Therefore, the goal of the present project was to integrate thyroid‐related endpoints for fish into a test protocol combining OECD TGs 229 (Fish Short‐Term Reproduction Assay) and 234 (Fish Sexual Development Test). The resulting “integrated Fish Endocrine Disruption Test” (iFEDT) was designed as a comprehensive approach to cover sexual differentiation, early development and reproduction and to be able to identify disruption not only of the sexual/reproductive, but also the TH system. Two 85 d exposure tests were performed using different well‐studied endocrine disruptors: propylthiouracil (PTU) and 17α‐ethinylestradiol (EE2). Whereas the companion part A of this study (Pannetier et al., 2023a) presents the findings on effects by PTU and EE2 on endpoints established in existing TGs, the present part B discusses effects on novel thyroid‐related endpoints such as TH levels, thyroid follicle histopathology as well as eye development. PTU induced a massive proliferation of thyroid follicles in any life‐stage, and histopathological changes of the eyes proved to be highly sensitive for TH system disruption especially in younger life‐stages. For measurement of THs, further methodological development is required. EE2 not only showed the well‐known disruption of the hypothalamic‐pituitary‐gonadal axis, but also induced effects on thyroid follicles in adult zebrafish (Danio rerio) exposed to higher EE2 concentrations, suggesting crosstalk between endocrine axes. The novel iFEDT has thus proven capable of simultaneously capturing endocrine disruption of both the steroid and thyroid endocrine systems.