Self-organization of donor and acceptor π-systems forms alternate D–A stacks of the donor and acceptor molecules. Using a photochromic π-switch as a donor and an electron deficient acceptor dye such stacks were formed. Photomodulation of the donor unit with visible light led to a photoisomerized state having a non-planar structure with reduced donor ability, thereby causing destruction of the alternate D–A π-stacks. The formation and destruction of the stacks were studied by various spectroscopy methods. Both the stacks and the depleted stacks were studied by DLS and SEM experiments. The regeneration of the stacks occurred in solution with the reversal of the photoisomerization process with ultraviolet light. Computational and differential scanning calorimetric studies validated the thermodynamics of the formation of the stacks. This work presents a reversible assembly–disassembly of a donor–acceptor π system devoid of additional auxiliary non-covalent bonding motifs in the donor and acceptor molecules.