New monodromy relations of loop amplitudes are derived in open string theory. We particularly study N-point (planar and non-planar) one-loop amplitudes described by a world-sheet cylinder and derive a set of relations between subamplitudes of different color orderings. Various consistency checks are performed by matching a alpha'-expansions of planar and non-planar amplitudes involving elliptic iterated integrals with the resulting periods giving rise to two sets of multiple elliptic zeta values. The latter refer to the two homology cycles on the once-punctured complex elliptic curve and the monodromy equations provide relations between these two sets of multiple elliptic zeta values. Furthermore, our monodromy relations involve new objects for which we present a tentative interpretation in terms of open string scattering amplitudes in the presence of a non-trivial gauge field flux. Finally, we provide an outlook on how to generalize the new monodromy relations to the non-oriented case and beyond the one-loop level. Comparing a subset of our results with recent findings in the literature we find therein several serious issues related to the structure and significance of monodromy phases and the relevance of missed contributions from contour integrations. (C) 2017 The Author(s).