A new tool for customization of layered double hydroxide nanoparticles (LDH-NPs) is described. The composition of the synthesis solutions determine LDH-NPs aggregation. Hydrothermal treatment duration is a key parameter to determine particle size. Fluorescein intercalation in LDH-NPs affected by OH– anions competition. Customized LDH-NPs for biological studies with GUVs and cell lines were synthesized.