The electrochemical molecular intercalation of two-dimensional layered materials (2DLMs) produces stable and highly tunable superlattices between monolayer 2DLMs and self-assembled molecular layers. This process allows unprecedented flexibility in integrating highly distinct materials with atomic/molecular precision to produce a new generation of organic/inorganic superlattices with tunable chemical, electronic, and optical properties. To better understand the intercalation process, we developed an on-chip platform based on MoS model devices and used optical, electrochemical, and in situ electronic characterizations to resolve the intermediate stages during the intercalation process and monitor the evolution of the molecular superlattices. With sufficient charge injection, the organic cetyltrimethylammonium bromide (CTAB) intercalation induces the phase transition of MoS from semiconducting 2H phase to semimetallic 1T phase, resulting in a dramatic increase of electrical conductivity. Therefore, in situ monitoring the evolution of the device conductance reveals the electrochemical intercalation dynamics with an abrupt conductivity change, signifying the onset of the molecule intercalation. In contrast, the intercalation of tetraheptylammonium bromide (THAB), a branched molecule in a larger size, resulting in a much smaller number of charges injected to avoid the 2H to 1T phase transition. Our study demonstrates a powerful platform for in situ monitoring the molecular intercalation of many 2DLMs (MoS, WSe, ReS, PdSe, TiS, and graphene) and systematically probing electronic, optical, and optoelectronic properties at the single-nanosheet level.