Correlated oxides can exhibit complex magnetic patterns. Understanding how magnetic domains form in the presence of disorder and their robustness to temperature variations has been of particular interest, but atomic scale insight has been limited. We use spin-polarized scanning tunneling microscopy to image the evolution of spin-resolved modulations originating from antiferromagnetic (AF) ordering in a spin-orbit Mott insulator perovskite iridate Sr3Ir2O7 as a function of chemical composition and temperature. We find that replacing only several percent of lanthanum for strontium leaves behind nanometer-scale AF puddles clustering away from lanthanum substitutions preferentially located in the middle strontium oxide layer. Thermal erasure and reentry into the low-temperature ground state leads to a spatial reorganization of the AF puddles, which nevertheless maintain scale-invariant fractal geometry in each configuration. Our experiments reveal multiple stable AF configurations at low temperature and shed light onto spatial fluctuations of the AF order around atomic scale disorder in electron-doped Sr3Ir2O7.