The two-dimensional electron system (2DES) located at the surface of strontium titanate (STO) and at several other STO-based interfaces has been an established platform for the study of novel physical phenomena since its discovery. Here we report how the interfacing of STO and tetracyanoquinodimethane (TCNQ) results in a charge transfer that depletes the number of free carriers at the STO surface, with a strong impact on its electronic structure. Our study paves the way for efficient tuning of the electronic properties, which promises novel applications in the framework of oxide/organic-based electronics.