We study the universal contributions to the entanglement entropy (EE) of 2+1d and 3+1d holographic conformal field theories (CFTs) on topologically non-trivial manifolds, focusing on tori. The holographic bulk corresponds to AdS-soliton geometries. We characterize the properties of these regulator-independent EE terms as a function of both the size of the cylindrical entangling region, and the shape of the torus. In 2+1d, in the simple limit where the torus becomes a thin 1d ring, the EE reduces to a shape-independent constant 2γ. This is twice the EE obtained by bipartitioning an infinite cylinder into equal halves. We study the RG flow of γ by defining a renormalized EE that 1) is applicable to general QFTs, 2) resolves the failure of the area law subtraction, and 3) is inspired by the F-theorem. We find that the renormalized γ decreases monotonically at small coupling when the holographic CFT is deformed by a relevant operator for all allowed scaling dimensions. We also discuss the question of non-uniqueness of such renormalized EEs both in 2+1d and 3+1d.