Non‐covalent functionalization of layered 2D materials is an essential tool to modify and fully harness their optical, electrical, and chemical properties. Herein, a facile method enabling the selective formation of self‐assembled monolayers (SAMs) of perylene bisimide (PBI) on transition metal dichalcogenides (TMDs), directly on the growth substrate (on‐chip), is presented. Laterally‐resolved infrared atomic force microscopy (AFM‐IR) and time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) are applied as superior techniques to gain detailed information beyond traditional surface analysis techniques, such as Raman spectroscopy and AFM, on TMD/PBI structures. The highly selective functionalization conducted in organic solution on MoS₂ and WSe₂ opens up a pathway to controllable, versatile functionalization of layered materials, which is highly sought after for its potential in passivation, tuning of …