This paper studies how many orthogonal bi-invariant complex structures exist on a metric Lie algebra over the real numbers. Recently, it was shown that irreducible Lie algebras which are additionally 2-step nilpotent admit at most one orthogonal bi-invariant complex structure up to sign. The main result generalizes this statement to metric Lie algebras with any number of irreducible factors and which are not necessarily 2-step nilpotent. It states that there are either 0 or 2(k) such complex structures, with k the number of irreducible factors of the metric Lie algebra. The motivation for this problem comes from differential geometry, for instance to construct non-parallel Killing-Yano 2-forms on nilmanifolds or to describe the compact Chern-flat quasi-Kahler manifolds. The main tool we develop is the unique orthogonal decomposition into irreducible factors for metric Lie algebras with no non-trivial abelian factor. This is a generalization of a recent result which only deals with nilpotent Lie algebras over the real numbers. Not only do we apply this fact to describe the orthogonal bi-invariant complex structures on a given metric Lie algebra, but it also gives us a method to study different inner products on a given Lie algebra, computing the number of irreducible factors and orthogonal bi-invariant complex structures for varying inner products.