We describe methodological aspects of halloysite clay nanotubes based core–shell design with integrated nano-, micro- and macrofeatures. Characterization of aluminosilicate mesoporous nanotubes physicochemical properties was given followed by principles of the halloysite modification. The halloysite coating with metal-containing structures is discussed, along with the selective formation of a metal-based core inside clay lumens. We give examples of nanoscale core–shell systems with metal, bimetal, metal oxides and salts nanoparticles, nanorods, nanosheets as well as ordered morphologies. The hybrid nanostructures with organic macromolecules and polymers covering clay tubes are proposed as active phase transfer catalysts, polymers fillers and sustain drug delivery systems. Liquid marbles and microorganisms covered with halloysite shells are described demonstrating eco-friendly and abundant tubular nanoclay applications for the bioremediation of oil spills.