We study the effect of a magnetic field on the low energy description of Mott insulators with strong spin-orbit (SO) coupling. In contrast to the standard case of the Hubbard model without SO coupling, we show that Peierls phases can modulate the magnetic exchange at leading order in the interaction. Our mechanism crucially depends on the existence of distinct exchange paths between neighboring magnetic ions enclosing a well-defined area. Thus it will generically be present in any solid state realisation of the Kitaev model and its extensions. We explicitly calculate the variation of the exchange constants of the so-called $JKGamma$ model as a function of the magnetic flux. We discuss experimental implications of our findings for various settings of candidate Kitaev spin liquids.
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