Driven by growing concerns regarding health and well-being, functional foods have gained prominence in recent years. Among them, chia (Salvia hispanica L.) stands out due to its composition of fatty acids and bioactive compounds such as phenolics associated with antioxidant properties. Proper crop management, particularly regarding phosphate fertilization, is crucial, as phosphorus plays an essential role in various metabolic processes, including nucleic acid synthesis, energy transfer, phospholipid formation, and the regulation of secondary metabolite production. Consequently, the availability of this nutrient can directly influence the nutritional quality of the seeds, making it important to evaluate this effect in both light- and dark-colored chia seeds. In this context, understanding chia's response to phosphate fertilization (P₂O₅) is vital for refining management practices and enhancing nutritional attributes relevant to the functional food market. This study aimed to evaluate the impact of phosphorus rates (0, 50, and 100 kg ha⁻¹) on the nutritional composition and the antioxidant and functional properties of dark (DS) and light (LS) chia seeds. Analyses were conducted regarding proximate composition, phenolic compounds, antioxidant activity, fatty acid profiles, and phytosterols. The results demonstrated that phosphate fertilization induced significant changes in the seeds' chemical characteristics, with distinct responses observed between the evaluated genotypes. Dark seeds showed a substantial increase in lipid content, ranging from 24 to 33 g 100 g⁻¹, while light seeds showed an increase from 29 to 34 g 100 g⁻¹ across the applied P₂O₅ rates. Both genotypes exhibited a reduction in carbohydrate content, amounting to approximately 28% for DS and 32% for LS. The results suggest that phosphorus application in chia fertilization may have favored a metabolic shift toward lipid synthesis, thereby reducing the carbohydrate fraction. Applying 100 kg ha⁻¹ of P₂O₅ increased protein content by 8.20% in light-colored seeds (DS) and by 13.62% in dark-colored seeds (LS). Phosphate fertilization promoted an increase in total phenolic compound levels for both DS (15.35–36.48%) and LS (47.33–98.66%), resulting in enhanced antioxidant activity. Analysis of the phenolic and organic acid profiles identified vanillin as the major compound, followed by nicotinic acid and rutin. Regarding fatty acids, linolenic acid (omega-3) predominated particularly in seeds treated with the highest P₂O₅ dose (100 kg ha⁻¹; 57 and 56 mg 100 g⁻¹ oil for DS and LS, respectively) demonstrating the influence of phosphorus on modulating lipid composition. Furthermore, phosphate fertilization positively influenced the phytosterol profile; β-sitosterol, campesterol, and stigmasterol were identified, with β-sitosterol predominating and showing higher levels in light-colored chia seeds. The results indicate that, among the tested P₂O₅ rates, the highest dose (100 kg ha⁻¹) is recommended to improve the nutritional and functional attributes of both light and dark chia seeds. Adequate phosphorus application enhances the seeds' added value, reinforcing the crop's potential within the functional food sector.