The extraordinary accumulation of cyanide ions within biological cells is a severe health risk. Detecting and tracking toxic cyanide ions within these cells by simple and ultrasensitive methodologies are of immense curiosity. Here, continuous tracking of ultimate levels of CN−-ions in HeLa cells was reported employing biocompatible branching molecular architectures (BMAs). These BMAs were engineered by decorating colorant-laden dendritic branch within and around the molecular building hollows of the geode-shelled nanorods of organic–inorganic Al-frameworks. Batch-contact methods were utilized to assess the potential of hollow-nest architecture for inhibition/evaluation of toxicant CN--ions within HeLa cells. The nanorod BMAs revealed significant potential capabilities in monitoring and tracking of CN− ions (88 parts per trillion) in biological trials within seconds. These results demonstrated sufficient evidence for the compatibility of BMAs during HeLa cell exposure. Under specific conditions, the BMAs were utilized for in-vitro fluorescence tracking/sensing of CN− in HeLa cells. The cliff swallow nest with massive mouths may have the potential to reduce the health hazards associated with toxicant exposure in biological cells.