Microgel particles and capsules which consist of multiple layers can be fabricated using droplet microfluidics, but in existing methods, emulsion templating forms layers of dissimilar polarity. In this paper, we fabricate functional microgel capsules that consist of two miscible yet distinct layers. We use microfluidic devices to template micrometer-sized drops that are loaded with prepolymerized precursors and solidify them through a polymer-analogous reaction. This allows the particle morphology to be controlled and prevents pronounced interpenetration of the different layers despite their miscibility. We use polyacrylamide and poly(N-isopropylacrylamide) precursors to form thermoresponsive core-shell microparticles and demonstrate their utility for encapsulation and controlled release applications.