Graphene-like two-dimensional transition metal dichalcogenides such as MoS₂, MoSe₂, MoTe₂, NbS₂, NbSe₂, WS₂, WSe₂, TaS₂ and TaSe₂ are emerging as promising new-generation materials because of their basic properties complementing those of graphene in practical applications. In this study, graphene-like MoS₂-modified magnetic carbon-dot nanoflowers (MoS₂@Fe₃O₄@C-dot NFs) were synthesized via a simple and green hydrothermal synthesis procedure. Carbon dots (C-dots) were obtained from cow's milk by a very simple one-step hydrothermal synthesis method. Owing to the fact that the sandwich layers of MoS₂ provide sufficient and effective intermediate layer spaces, a large number of magnetic C-dots can easily enter these spaces between the layers. A MoS₂ aqueous solution has good chemical stability and dispersibility in acidic, basic and organic solvents. There is a mutually beneficial relationship between MoS₂, C-dots and Fe₃O₄ particles. Magnetic carbon dots (Fe₃O₄@C-dots) prevent MoS₂ layers from agglomerating, while the chemically very stable MoS₂ layers act as a protective layer on magnetic carbon dots. In addition, the –OH and –COOH functional groups of the C-dots lead to improvements in the extraction efficiency of the adsorbent due to the formation of a hydrogen bond between these groups and ibuprofen. Hence, the MoS₂@Fe₃O₄@C-dot NFs as sorbents for the MSPE procedure showed good extraction performance. The new MoS₂@Fe₃O₄@C-dot NFs were used as magnetic solid-phase extraction (MSPE) adsorbents for the separation and enrichment of ibuprofen from pharmaceutical, environmental water and synthetic urine samples before high pressure liquid chromatography (HPLC-DAD) determination. MoS₂@Fe₃O₄@C-dot NFs were characterized using X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), Raman spectroscopy and SEM-mapping techniques. The optimization of analytically important variables such as pH, adsorbent amount, eluent type and volume, sample volume and extraction time was performed. In the experiments performed, the recoveries of ibuprofen from pharmaceutical, environmental water and synthetic urine samples were in the range of 89–105%. The limit of detection (LOD), limit of quantification (LOQ) and preconcentration factor (PF) were found to be 11 × 10⁻⁶ μg mL⁻¹, 34 × 10⁻⁶ μg mL⁻¹ and 100, respectively. The relative standard deviation values within the day (intra-day) and between days (inter-day) were calculated to be 1.29% and 3.19%, respectively.