The Fermi-Löwdin orbital self-interaction correction (FLOSIC) method effectively provides a transformation from canonical orbitals to localized Fermi-Löwdin orbitals which are used to remove the self-interaction error in the Perdew-Zunger (PZ) framework. This transformation is solely determined by a set of points in space, called Fermi-Löwdin descriptors (FODs), and the occupied canonical orbitals or the density matrix. In this work, we provide a detailed workflow for the implementation of the FLOSIC method for removal of self-interaction error in DFT calculations in an orbital-by-orbital basis that takes advantage of the unitary invariant nature of the FLOSIC method. In this way, it is possible to cast the self-consistent energy minimization at fixed FODs in the same manner than standard Kohn-Sham with one additional term in the Kohn-Sham Hamiltonian that introduces the PZ self-interaction correction. Each energy minimization iteration is divided in two substeps, one for the density matrix and one for the FODs. Expressions for the effective Kohn-Sham matrix and FOD gradients are provided such that its implementation is suitable for most electronic structure codes. We analyze the convergence characteristics of the algorithm and present applications for the evaluation of NMR shielding constants and real-time time-dependent DFT simulations based on the Liouville-von Neumann equation to calculate excitation energies.