The chemical modification of an immobilized single crystal in a fluid cell is reported, whereby a material with switching functions is generated in situ by generating a chemical reagent in the flow. Crystals of the insulating organic crystal of TCNQ (tetracyanoquinodimethane) were grown in a microfluidic channel and were trapped using a pneumatic valve, a nascent technique for materials manipulation. They were subsequently reduced using solution-deposited silver to provide a conducting material in situ by a heterogeneous reaction. Removal of the new material from the chip proved it to be the silver salt of reduced TCNQ. Uniquely, conducting atomic force microscope (CAFM) studies show three regions in the solid. The localized original neutral organic material crystal is shown to be an insulator but to produce areas with Ohmic conducting characteristics after reduction. This inhomogeneous doping provides an opportunity for probing electrical materials properties side by side. Measurements with the CAFM witness this conducting material where the TCNQ is fully transformed to the silver salt. Additionally, an intermediate phase is observed that exhibits bipolar resistive switching typical of programmable resistive memories. Raman microscopy proves the conversion of the material in specific regions and clearly defines the intermediate phase region that could be responsible for the switching effect in related materials. This kind of “on crystal chemistry” exploiting immobilization and masking by a pneumatic clamp in a microfluidic channel shows how material can be selectively converted to give different functionalities in the same material piece, even though it is not a single crystal to single crystal conversion, and beckons exploitation for the preparation of systems relevant for molecular electronics as well as other areas where chemical manipulation of single crystals could be beneficial.