Colossal magnetoresistance is a dramatic decrease in resistivity caused by applied magnetic fields, and has been the focus of much research because of its potential for magnetic data storage using materials such as manganites. Although extensive microscopy and theoretical studies have shown that colossal magnetoresistance involves competing insulating and ferromagnetic conductive phases, the mechanism underlying the effect remains unclear. Here, by directly observing magnetic domain walls and flux distributions using cryogenic Lorentz microscopy and electron holography, we demonstrate that an applied magnetic field assists nucleation and growth of an ordered ferromagnetic phase. These results provide new insights into the evolution dynamics of complex domain structures at the nanoscale, and help to explain anomalous phase separation phenomena that are relevant for applications. Our approach can also be used to determine magnetic parameters of nanoscale regions, such as magnetocrystalline anisotropy and exchange stiffness, without bulk magnetization results or neutron scattering data.