In this study, we evaluated zinc (Zn) and selenium (Se) biofortification in strawberry fruits under substrate and soil cultivation, along with their effects on mineral element accumulation and fruit quality. To achieve this, foliar Zn (0.1% and 0.2%) and Se (0.003% and 0.006%) fertilizers were applied separately or in combination at the initial flowering stage. The Zn and Se contents in strawberry fruits increased with the spraying dosage. Compared to the control, the Zn content in the first batch of Zn-treated strawberries increased by 36.9–109% and 27.1–102% under substrate and soil cultivation, respectively, while Se increased by 313–444% and 21.3–53.3%, respectively. However, foliar Zn application could not ensure long-term sustainability as Zn in strawberries gradually decreased in the two subsequent batches, while Se was more stable. Compared to the control, the Se content in the three batches of Se2 (0.006%)-treated strawberries grown in soil increased by 32.9%, 124%, and 109%, respectively. Meanwhile, compared to Se alone, the Zn–Se combined application decreased the Se content in strawberries by 61.2–77.6% and 24.9–45.7% under substrate and soil cultivation, respectively, while low doses of Se promoted Zn enrichment (by 8.62–40.9%) and high doses inhibited it (by 13.2–28.9%) under substrate cultivation. Moreover, the copper content in strawberries under substrate cultivation after the Se1 (0.003%) treatment was significantly higher (by 75.0%) than that in the control. A positive correlation was observed between Cu and Zn contents in strawberries under both substrate and soil cultivation. A consistent positive impact was also observed on fruit quality. The Se2 (0.006%) treatment caused an increase in ascorbic acid content (by 37.2%) in strawberry fruits. The soluble sugar content increased by 36.3% after the Zn1 (0.1%) treatment. The present study provides a practical basis for the biofortification of strawberries with Zn and Se.
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