A novel GC/MS analytical procedure for the identification of lipids, waxes, proteins, and resinous materials in the same microsample from painted works of art has been optimized. It is based on a sample multistep chemical pretreatment (solvent extractions and microwave-assisted chemolysis) that is able to separate the various organic components into different fractions, which are suitably treated and derivatized before analysis. In particular, the procedure allows the complete saponification of wax esters and the completeness of the Cannizzaro type reaction of shellac acids in conditions that are suitable also for glycerides saponification. The method was tested on reference materials for the identification of proteinaceous binders (egg, collagen, casein) on the basis of the quantitative determination of the amino acid profile and the identification of glycerolipids (linseed oil, poppy seed oil, walnut oil, and egg), plant resins (Pinaceae resins, sandarac, mastic, and dammar), animal resins (shellac), tars or pitches, and natural waxes (beeswax, carnauba wax) on the basis of the determination of fatty acid, alcohol, and hydrocarbon profiles and of significant terpenic molecular markers. The procedure was applied to the characterization of three old paint microsamples. Animal glue, egg, linseed oil, beeswax, Pinaceae resin, dammar, and shellac were the identified materials found in mixtures and recognized as original and/or restoration substances.