<p>Early life stress is key in development and behaviour and may have long-term effects, as it represents a window of increased vulnerability. In our study we evaluated two stressors, temperature and photoperiod —alone and combined—, in zebrafish (<i>Danio rerio</i>) larvae up to 120 h post-fertilisation. The objective of this study was to investigate the effects of non-lethal environmental stressors and their potential synergistic effects until completion of organogenesis integrating molecular, cellular and behavioural analyses. Larvae were subjected to 4 experimental conditions: “control” (C) (14 h light: 10 h darkness; <i>T</i> = 27 ± 1 °C); “heat shock” (HS) (14 h light: 10 h darkness; <i>T</i> = 34 °C); “darkness” (D) (24 h darkness; <i>T</i> = 27 ± 1 °C) and “stressed” (S⁺) (24 h darkness; <i>T</i> = 34 °C). Our results confirmed phenotypic, behavioural and molecular alterations. The S⁺ larvae showed a lower survival curve, lower regeneration, a higher number of malformations, predominantly those related to the swim bladder, lower motor activity and a dysregulation of <i>miR29a</i> and <i>clocka</i>, <i>hspa9</i>, <i>hspa5</i> and <i>cxcr4b</i> genes. The results revealed a similar number of Ddx4⁺ cells between groups but non-canonical migration patterns in the S⁺ group. This integrated approach offers new insights into the molecular mechanisms underlying the stress response during embryogenesis and provides a new perspective on the interaction between temperature and light on early-stage development.</p>