**Background:** Modern Atlantic salmon feeds rely heavily on plant ingredients, which can reduce fish performance and health compared to marine-based feeds. Trace minerals (Cu, Fe, Mn, Se, Zn) are essential for numerous physiological processes, but their bioavailability and effects depend on chemical form (organic vs. inorganic) and dietary level. This study aimed to map the physiological implications of supplemental essential trace minerals in Atlantic salmon smolt, focusing on growth, health, welfare, tissue assimilation, and potential environmental impacts.
**Methods:** A 2 × 4 factorial design was used with two mineral sources (organic [OM] vs. inorganic [IM]) and four dietary supplementation levels (1st to 4th). The organic minerals were Bioplex Cu, Mn, Zn, Fe and Selplex (Alltech Inc.); inorganic minerals were sulphates. Target supplementation levels were: Cu 10–25 mg/kg, Fe 348–550 mg/kg, Zn 88–180 mg/kg, Mn 57–100 mg/kg, Se 0.85–1.00 mg/kg. Eight experimental diets were produced by extrusion and fed to triplicate groups of Atlantic salmon smolt (initial weight 215 ± 1.36 g) for 83 days. Fish were subjected to handling stress in weeks 6–8. Samplings included blood chemistry, tissue mineralisation, whole-body fatty acid profile, fillet technical quality, bone strength, skin histology, and midgut transcriptome (microarray). Apparent digestibility coefficients (ADC) and retention efficiency (RE) were calculated using yttrium oxide as an inert marker.
**Key Results:** Fish fed OM showed significantly higher growth rate at weeks 6 and 7 (p < 0.05) and a tendency for higher final body weight (p = 0.087) and total feed intake (p = 0.080) compared to IM. Mineral ADC was generally higher at the lowest supplementation level; Se ADC increased with supplementation in IM but decreased in OM (interaction p < 0.001). Zn ADC was approximately 6% higher in IM (p = 0.033). Phosphorus ADC decreased with increasing IM supplementation but remained constant in OM. Retention efficiency of Se was significantly higher in OM (highest 42.9% in OM1) vs. IM (lowest 13.2% in IM2) (p = 0.041 for interaction). Cu, Fe, Mn, and Zn RE decreased with increasing supplementation level. Whole-body EPA and DHA were significantly higher in OM (EPA p = 0.003; DHA p = 0.026). Omega-6/omega-3 ratio was lower in OM (p < 0.001). Slaughter yield was significantly higher in OM (p < 0.001), and fillet yield tended to be higher (p = 0.084). Bone strength increased with OM level (p < 0.04). Fillet gaping after thawing was lowest at OM4. Blood serum cortisol was significantly lower in OM after first handling stress (p = 0.023). Midgut transcriptome showed coordinated changes in lipid metabolism genes and downregulation of immune genes, stronger in IM (p = 2.1 × 10⁻⁷).
**Clinical Implications:** Organic trace mineral supplementation improves growth, selenium retention, fillet yield, and fatty acid profile (higher EPA+DHA) in Atlantic salmon smolt, while reducing phosphorus excretion and potentially lowering environmental impact. The study recommends lower supplementation levels for organic minerals (Cu 10–15 ppm, Fe ≤348 ppm, Mn 57–71 ppm, Zn 88–119 ppm, Se 0.85 ppm) compared to inorganic (Zn 119–149 ppm, Se 0.9–0.95 ppm). These findings support the use of organic minerals to enhance fish welfare, product quality, and sustainability in salmon aquaculture.