We report the effect of alkyl side chain branching on melt-recrystallization of nanoconfined polypeptoid films using poly(N-octyl glycine) (PNOG) and poly(N-2-ethyl-1-hexyl glycine) (PNEHG) as model systems. Upon cooling from the isotropic melt, confined PNOG molecules recrystallize into a near-perfect orthorhombic crystal structure with the board-like molecules stacked face-to-face in the substrate-parallel direction, resulting in long-range ordered wormlike lamellae that occupy the entire film. By contrast, rod-like PNEHG molecules bearing branched N-2-ethyl-1-hexyl side chains stack into a columnar hexagonal mesophase with their backbones oriented parallel to the substrates, forming micron-sized sheaf-like superstructures under confinement, exposing large areas of empty spaces in the film. These findings highlight the effect of alkyl side chain branching on the packing motif and multiscale crystalline structure of polypeptoids under a nanoconfined geometry.