Programming the organization of π-conjugated systems into nanostructures of defined dimensions is a requirement for the preparation of functional materials. Herein, we have achieved high-precision control over the self-assembly pathways and fiber length of an amphiphilic BODIPY dye in aqueous media by exploiting a programmable hydrogen bonding lock. The presence of a (2-hydroxyethyl)amide group in the target BODIPY enables different types of intra- vs. intermolecular hydrogen bonding, leading to a competition between kinetically controlled discoidal H-type aggregates and thermodynamically controlled 1D J-type fibers in water. The high stability of the kinetic state, which is dominated by the hydrophobic effect, is reflected in the slow transformation to the thermodynamic product (several weeks at room temperature). However, this lag time can be suppressed by the addition of seeds from the thermodynamic species, enabling us to obtain supramolecular polymers of tuneable length in water for multiple cycles.