Halloysite is a promising building block in nanoarchitectonics of functional materials, especially in the development of novel biomaterials and smart coatings. Understanding the behavior of materials produced using halloysite nanotubes within living organisms is essential for their safe applications. In this study, quantum dots of different compositions were synthesized on the surface of modified clay nanotubes, and the biodistribution of this hybrid material was monitored within Caenorhabditis elegans nematodes. The influence of the modification agent as well as the particles’ composition on physicochemical properties of hybrid nanomaterials was investigated. Several microscopy techniques, such as fluorescence and dark-field microscopy, were compared in monitoring the distribution of nanomaterials in nematodes’ organisms. The effects of QDs-halloysite composites on the nematodes’ life cycle were investigated in vivo. Our fluorescent hybrid probes induced no acute toxic effects in model organisms. The stable fluorescence and low toxicity towards the organisms suggest that the proposed synthesis procedure yields safe nanoarchitectonic materials that will be helpful in monitoring the behavior of nanomaterials inside living cells and organisms.