The magnetic field induced rearrangement of the cycloidal spin structure in ferroelectric mono-domain single crystals of the room-temperature multiferroic BiFeO$_3$ is studied using small-angle neutron scattering (SANS). The cycloid propagation vectors are observed to rotate when magnetic fields applied perpendicular to the rhombohedral (polar) axis exceed a pinning threshold value of $\sim$5\,T. In light of these experimental results, a phenomenological model is proposed that captures the rearrangement of the cycloidal domains, and we revisit the microscopic origin of the magnetoelectric effect. A new coupling between the magnetic anisotropy and the polarization is proposed that explains the recently discovered magnetoelectric polarization to the rhombohedral axis.