Nanotechnology, as a discipline, has been driven in part by the motivation to generate materials with diverse functionalities, such as self-healing fabrics, flexible display monitors, and colloidal solar cells. To address the demand for new and novel nanomaterials, efficient fabrication methods are required not only to synthesize nanoscale building blocks, but also achieve controlled assemblies of these structural units into functional architectures. One area of growing interest in nanomanufacture has been to create bi-functional materials such as particles or fibers in which the surface consists of two regimes with unique physical or chemical properties, often referred to as “Janus” materials. To date, an impressive number of methods have been developed to fabricate spherical Janus particles, including microfluidic emulsification, electrospray, and self-assembly at liquid interfaces. Recently, this work has been extended to the fabrication on Janus nanofibers, implementing methods such as traditional syringe-based electrospinning methods and hybrid microfluidic devices consisting of microfluidic manifolds and stainless steel tubes. While effective techniques, they remain labor intensive and require substantial technical expertise to implement. Addressing the need for a robust, scalable methodology for Janus nanofiber synthesis, we have developed monolithic poly(dimethylsiloxane)-based microfluidic manifolds capable of parallel electrospinning of Janus nanofibers. Using branching microchannel architecture, flow rates of the individual polymeric fiber components are regulated using a syringe pump, with the two solutions merging at the multiple microfluidic outlets in a sharp bi-phasic, side-by-side orientation prior to electrospinning. With microfluidics-based manifolds, biphasic Janus nanofibers of poly (vinylpyrrolidone) (PVP) + Polypyrrole (PPy) /PVP nanofibers with an average diameter of 250 nm were successfully fabricated using elastomeric microfluidic devices. Fiber characterization and confirmation of the Janus morphology was subsequently carried out using a combination of scanning electron microscopy, energy dispersion spectroscopy and transmission electron microscopy.