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• Naturally available 3D diatoms (DE) combined with MIL100(Fe) to form MIL100(Fe)-DE hybrid materials. • MIL100(Fe)-DE as drug carrier controlled the drug release up to 23 days. • MIL100(Fe)-DE used as heterogeneous Fenton's catalysis showed 99% of MB degradation efficiency. • MIL100(Fe)-DE showed Pb2+ removal of 96.45% efficiency and high adsorption capacity of 155 mg/g with excellent reusability. • MIL100(Fe)-DE explored for various dye removal applications with removal efficiency of 98, 96, 76 and 75% respectively. Metal-organic frameworks (MOFs) emerged as one of the promising functional materials for broad applications. To improve the sustainability of their synthetic route and extend their applications are still demanding and challenging task. Herein, to address this problem, we report practical use of "eco-friendly" approach to create new type of hybrid materials by combining MOFs with naturally available hierarchical diatom biosilica (DE) acts as 3D porous scaffolds. This combination of high surface area, an unique 3D diatom architecture with 2D MOFs structure with specific chemical functionalities –OH, –COOH and Fe atoms confined in MIL-100(Fe)-DE hybrid materials and explored for a wide range of applications like drug delivery, catalyst support and environmental adsorbents. To prove drug delivery application for MIL-100(Fe)-DE, isoniazid (INH) anti-TBC (tuberculosis) drug is selected as typical drug model showing an enhanced drug loading capacity of 9.6 ± 1.6% and an extended in vitro controlled drug release performances over 23 days. This is significant improvement of short drug release characterstics and biological half life of INH (1–4 h) that limits to rich full therapeutic benefits for treatment of TBC. A heterogeneous Fenton's catalysis study of MIL-100(Fe)-DE showed a rapid degradation of Malachite green (MG) dye within 60 min with degradation efficiency of 99.02 ± 1.3%. To prove environment remediation performances at 25 °C and in pH 6, MIL-100(Fe)-DE displayed efficient removal of Pb2+ with removal efficiency of 96.45 ± 2.1%, high adsorption capacity of 155 mg/g and the improved partition co-efficient (PC) was 87.32 mg.g−1.µM−1 for Pb2+ of (50 mg/L) with excellent reusability. Finally, MIL-100(Fe)-DE hybrid was tested for the removal of cationic dyes such as methylene blue (MB), rhodamine B (RhB) and anionic dyes like congo red (CR) and erichrome black T (EBT) showing 96.10 ± 1.3, 75.11 ± 1.95, 98.11 ± 1.7 and 76 ± 1.88% of removal efficiency respectively. [ABSTRACT FROM AUTHOR]