The analysis and characterization of hybrid organic-inorganic metal oxide nanomaterials is of huge interest nowadays, due to their vastly increased use in current-issue applications reaching from solar energy conversion to catalysis or medical applications. Common to all, those hybrid materials are backboned by nanostructured metal oxides which contain modifications like self-assembled monolayers or molecule (e.g., drug) loadings leading to complex functional composite materials. While the chemical composition analysis or morphological studies of such structures can be performed superficially for example with time-of-light secondary ion mass spectrometry (TOF-SIMS) or scanning electron microscopy (SEM) respectively, a proper and efficient way for gathering depth information of such a composite material with appropriate resolution and measurement time has not yet been developed. Depth analysis by common sputtering techniques may lead to artefacts and destruction of molecular information during the analysis and, thereto, in a loss of signal. To overcome these issues in in-depth characterization of interlaced organic-inorganic nanostructures, this study presents the possibilities given by use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) alone and in combination with cross-section-polishing (CSP) or focused-ion-beam (FIB) milling. A correlation in-between those methods is demonstrated on a model zirconium dioxide nanostructure-based material and a complex model consisting of encapsulated dye sensitized solar cells based on titanium dioxide nanotubes.