Techniques are provided for authenticating a user using molecular snapshots of the user. One method comprises obtaining enrollment information of a user, wherein the enrollment information comprises a reference molecular snapshot of the user obtained following an ingestion by the user of nanoparticles; initiating a challenge to the user in connection with an authentication request by the user to access a protected resource; processing a responsive molecular snapshot obtained in response to the challenge, wherein the processing comprises evaluating the responsive molecular snapshot obtained in response to the challenge relative to the reference molecular snapshot; and resolving the authentication request based on the evaluating. The ingested nanoparticles optionally target one or more predefined cell types, and wherein the resolving further comprises the step of evaluating a ratio of cell types in the responsive molecular snapshot.