Ecological networks such as food webs are extremely complex and can provide important information about the robustness and productivity of an ecosystem. In most cases, it is not feasible to observe trophic interactions between predators and prey directly and with the available methods, it is difficult to quantify the connections between them. Here, we show that submicron-sized silica particles (100–150 nm) with encapsulated DNA (SPED) enable accurate food and organism labelling and quantification of specific animal-to-animal transfer over more than one trophic level. We found that SPED were readily transferable and quantifiable from the bottom to the top of a two-level food chain of arthropods. SPED were taken up in the gut system and remained persistent in an animal over several days. When uniquely labelled SPED were applied at predefined ratios, we found that information about their relative abundance was reliably conserved after trophic level transfer and over time. SPED were also applied to investigate the flower preference of fly pollinators and proved to be a fast and accurate analysis method. SPED combine attributes of DNA barcoding and stable isotope analysis such as unique labelling, quantification via real-time PCR and exact backtracking to the tracer source. This improves and simplifies the analysis and monitoring of ecological networks.