Correlated oxides can exhibit complex magnetic patterns, characterized by domains with vastly different size, shape and magnetic moment spanning the material. Understanding how magnetic domains form in the presence of chemical disorder and their robustness to temperature variations has been of particular interest, but atomic-scale insight into this problem 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 Sr3Ir2O7 as a function of chemical composition and temperature. We find that replacing only several percent of La for Sr leaves behind nanometer-scale AF puddles clustering away from La substitutions preferentially located in the middle SrO layer within the unit cell. Thermal erasure and re-entry into the low-temperature ground state leads to a spatial reorganization of the AF modulations, indicating multiple stable AF configurations at low temperature. Interestingly, regardless of this rearrangement, the AF puddles maintain scale-invariant fractal geometry in each configuration. Our experiments reveal spatial fluctuations of the AF order in electron doped Sr3Ir2O7, and shed light on its sensitivity to different types of atomic-scale disorder.