Conductance through single-molecule junctions, consisting of nanoparticle/molecule/nanoparticle units between nanoscale planar electrodes, was monitored in real time during several process sequences, including dielectrophoretic directed self-assembly and post-assembly modification. Assembly faults are directly detected in real time when non-ideal assembly conditions result in molecular junction failure and nanoparticle fusion in the junction. The real-time conductivity measured through the junction was sensitive to ambient conditions, and changes persisted over several days of exposure. Atomic layer deposition of Al2O3 was used to encapsulate and isolate the molecular junctions, and the effect of the deposition process sequence on current through the junction was evaluated in real time. Results indicate that the current measured during atomic layer deposition is sensitive to the chemical oxidation and reduction reactions proceeding in the 1-2 nm confined region between assembled nanoparticles.