This dataset originates from an intergenerational crude oil exposure experiment involving Atlantic cod (Gadus morhua) broodstock. Mature cod in late gametogenesis were exposed for 20 days to either a water-soluble fraction of crude oil or untreated seawater. The water-soluble fraction was generated using an oiled gravel column setup, resulting in an initial total PAH (polycyclic aromatic hydrocarbon) concentration (sum of 44 PAHs) of 97 μg/L, which declined to 17 μg/L by the end of the exposure period. Sixteen days after the end of the exposure, the fish were strip-spawned, and in vitro cross-fertilization was used to produce four distinct offspring lineages: control (unexposed parents), maternally exposed, paternally exposed and biparentally exposed. Embryos were reared in clean seawater until larval stages (42 days post fertilization). The dataset includes a variety of data types: rearing water temperature, body burden analysis of crude oil related compounds in freshly fertilized eggs and in embryos at 4 days post fertilization and embryo and larval phenotypic data, including egg diameter, hatching success, morphology, axial deformation, cardiotoxicity and larval survival. This dataset does not include transcriptomic (RNA-seq) data. However, quantitative real-time PCR (qPCR) data generated to validate the RNA-seq findings are included. The transcriptomics data generated is deposited separately (see Related Dataset). This experiment was conducted at the Tromsø Aquaculture Research Station (Havbruksstasjonen i Tromsø AS, Kårvik) and the Centre for Marine Aquaculture (CAM, NOFIMA AS, Kraknes), and was approved by the Norwegian Animal Research Authority (ID 22461).