Polyelectrolyte capsules (PECs) are a promising delivery system that has the ability to carry a large payload of a variety of cargoes. Controlling PEC properties is critical to understanding and tuning their cellular uptake efficiency, kinetics, and mechanism as well as their biodistribution in the body. The lack of a method to independently engineer PEC size, shape, and chemistry impedes both basic understanding of how physicochemical parameters affect PEC behavior in drug delivery and other applications, and the ability to optimize parameters for best function. Here, we report the successful fabrication of PECs having constant surface chemistry with independently controlled size and shape by combining soft organic templates created by the particle stretching method and a modified layer-by-layer (LBL) deposition process. Changing the template dispersion solution during LBL deposition from water to ethanol allowed us to overcome previous issues with organic templates, such as aggregation and template removal. These results will contribute not only to the basic study of the role of capsule shape and size on its function but also to the optimization of capsule properties for drug or imaging carriers, sensors, reactors, and other applications.