In the present study, an environmentally friendly magnetic dispersive micro-solid phase extraction was developed based on magnetic agarose nanoparticles and deep eutectic solvents for the isolation and pre-concentration of three flavonoids (morin, quercetin, and kaempferol) from dark tea, chocolate, vegetable, and fruit juice samples. In this method, deep eutectic solvents were synthesized from less toxic and low-cost substances under feasible conditions and used as eluents in the desorption process. These solvents can be considered as a green alternative to traditional organic reagents to increase the adsorption capacity and reduce the matrix interferences, dangerous waste generation and environmental pollution. A Plackett-Burman design was employed for screening the experimental variables. The effective variables were then optimized by Box-Behnken design (BBD). Under the optimial conditions, the presented method demonstrated wide linear ranges of 1–500 μg. L 1 for morin and quercetin, and 5–500 μg. L 1 for kaempferol with satisfactory recoveries above 91%. Limit of detections (LODs) and quantifications (LOQs) of flavonoids varied in 0.2–1.1 μg. L 1 and 0.66–3.63 μg. L 1, respectively. The precision of the proposed method was the range of 2.6–5.7%.