We study low energy magnetic transitions in nuclei of mass A=2, 3, namely the magnetic moments of the deuteron, Triton and Helium-3, and the thermal neutron radiative capture cross section. The calculation uses a consistent perturbative approach to describe the structure and dynamics of the reactions using effective field theory without pions up to next-to-leading order, making use of the low characteristic momentum of the reaction and the involved nuclei. We introduce a novel uncertainty assessment to estimate truncation effects, which enables us to estimate the theoretical uncertainty of the theory.