Engineered nanomaterials are often compositionally indistinguishable from their natural counterparts and thus their tracking in the environment or within biota requires the development of appropriate labelling tools. Stable isotope labelling has become a well-established such tool, developed to assign “ownership” or “source” to engineered nanomaterial enabling their tracing and quantification, especially in complex environments. A particular methodological challenge for the stable isotope labelling is to ensure the label is traceable in a range of environmental scenarios but without inducing modification of the properties of the nanoamaterial and without loss of signal from the label, thus retaining realism and relevance. This protocol describes the strategy for stable isotope labelling of several widely used metal and metal oxide nanomaterials, namely ZnO, CuO, Ag, and TiO2, using isotopically enriched precursors, namely 67Zn or 68Zn metal, 65CuCl2, 107Ag or 109Ag metal, and 47 TiO2 powder. A complete synthesis requires 1 to 8 days depending on the type of nanomaterial, the precursors used and the synthesis methods adopted. The physicochemical properties of the labeled particles are determined by optical, diffraction and spectroscopic techniques for quality control. The procedures for tracing the labels in aquatic (snail and mussel) and terrestrial (earthworm) organisms and monitoring the environmental transformation of labelled silver nanomaterials are also described. We anticipate this labelling strategy can be adopted by industry to facilitate applications such as nanosafety assessments before nanomaterials enter the market and environment as well as product authentication and tracking.