High‐density magnetic memories are essential components for spintronics, quantum computing, and energy‐efficient electronics. Miniaturization of magnetic storage units requires reduced dimensionality and magnetic domain stability at the nanoscale. However, inducing magnetic order and selectively tuning spin‐orbital coupling at specific locations is challenging. Here, an unprecedented approach is demonstrated to construct switchable magnetic nanoislands in a nonmagnetic matrix based on cobaltite homostructures. The magnetic and electronic states are laterally modified by epitaxial strain, which is regionally controlled by freestanding membranes. Tensile‐strained cobaltite layers exhibit ferromagnetic properties, while compressively strained cobaltite layers exhibit a small magnetic response to applied fields. The minimum size of magnetic nanoislands reaches ≈35 nm in diameter, suggesting the highest possible areal density can reach upto ≈400 Gbit/in2. This methodology provides an ideal platform for precisely controlled read/write schemes and enables scalable and patterned memories on silicon and flexible supports for various applications.