Electron Beam Induced Current (EBIC) is a Scanning Electron Microscope (SEM)-based technique that can provide information on the electrical properties of semiconductor materials and devices. This work focuses on the design and implemenation of an EBIC system in a dedicated Scanning Transmission Electron Microscope (STEM). The STEM-EBIC technique was used in the characterization of an Indium Gallium Nitride (InGaN) quantum well Light Emitting Diode (LED). The conventional “H-bar” Transmission Electron Microscopy (TEM) sample preparation method using Focused Ion Beam Micromachining (FIBM) was adapted to create an electron-transparent membrane approximately 300 nm thick on the sample while preserving the electrical activity of the device. A STEM-EBIC sample holder with two insulated electrical feedthroughs making contact to the thinned LED was designed and custom made for these experiments. The simultaneous collection of Z-contrast images, EBIC images, and In and Al elemental images allowed for the determination of the p-n junction location, AlGaN and GaN barrier layers, and the thin InGaN quantum well layer within the device. The relative position of the p-n junction with respect to the thin InGaN quantum well was found to be (19 ± 3) nm from the center of the InGaN quantum well.