<p>Pugheadedness and shortened lower jaw are frequent abnormalities in reared fish, developing during the early life period up to metamorphosis. In this study, we examined whether these abnormalities in gilthead seabream (<i>Sparus aurata</i> Linnaeus, 1758) could recover during the on-growing period. Furthermore, we examined whether jaw abnormalities affect fish survival and growth rates. At 123&#xa0;days post-hatching (dph, ca 5.0–7.5&#xa0;cm standard length, SL), 197–204 seabream juveniles with normal (Nor), pugheaded (UpJ), and shortened lower jaw (LoJ) phenotype were introduced in a common rearing tank. At 162 dph (8.0 ± 0.7&#xa0;cm SL), fish were pit-tagged and transferred to a sea cage for on-growing up to 514 dph (23.8 ± 1.4&#xa0;cm SL). Following the morphological examination of fish at 162 and 514 dph, pugheaded individuals were classified into two morphotypes, with (UpJ-Kub) or without (UpJ-Par) gross defects on the maxillary and premaxillary bones. During the on-growing period, 30.4% of the UpJ-Par fish turned into a normal phenotype. No recovery was observed in LoJ and UpJ-Kub juveniles. Geometric morphometric analysis revealed no significant differences in the head shape between the UpJ-Par fish with a recovered phenotype (Rec) and the normal group (<i>p</i> &gt; 0.05, Procrustes distance). A three-landmark-based angle on the snout area was effective in discriminating the normal juveniles (An_sn &gt; 148°) from 62.5% of the UpJ-Par fish without a recovery potential. LoJ, but not pugheadedness, had a significant negative effect on fish growth (<i>p</i> &lt; 0.05, ANOVA) and survival rates (<i>p</i> &lt; 0.05, <i>G</i>-test). The findings are discussed in terms of their practical application for quality control and the removal of abnormal fish in commercial hatcheries.</p>