We report the assembly of low-fouling polymer capsules with engineered deconstruction properties by using a combination of layer-by-layer (LbL) assembly and click chemistry. Preformed, hydrogen-bonded multilayers of alkyne-functionalized poly(N-vinyl pyrrolidone) (PVPON(Alk)) and poly(methacrylic acid) (PMA) assembled at pH 4 on silica particles were cross-linked with a bisazide linker (containing a disulfide link) through alkyne-azide click chemistry. Following dissolution of the silica template particles, and altering the solution pH to 7.2 to disrupt hydrogen bonding between PVPON(Alk) and PMA to effect removal of PMA, stable, cross-linked PVPON capsules were obtained. The presence of the disulfide bond in the bisazide linker endowed the PVPON capsules with degradable characteristics under model intracellular conditions. The capsules deconstructed within 4 h in the presence of 5 mM glutathione. The cross-linked PVPON(Alk) multilayers (assembled on silica particles) were low-fouling to a range of proteins, including fibrinogen, lysozyme, immunoglobulin G, and bovine serum albumin. Further, MTT assays showed that the PVPON capsules had no effect on the proliferation of cells from a human colon cancer cell line (LIM1899), indicating negligible cytotoxicity toward the LIM1899 cells. The low-fouling, degradable, and low cytotoxicity characteristics of the PVPON capsules makes them attractive as a platform for the development of advanced therapeutic delivery systems.