We calculate the lifetime of the deuteron from dimension-six quark operators that violate baryon number by one unit. We construct an effective field theory (EFT) for $|\mathrm{\Delta }B|=1$ interactions that give rise to nucleon and $\mathrm{\Delta }B=1$ deuteron decay in a systematic expansion. Nucleon decay introduces imaginary parts in the low-energy constants of the $\mathrm{\Delta }B=0$ nuclear interactions in Chiral EFT. We show that up to and including next-to-leading order the deuteron decay rate is given by the sum of the decay rates of the free proton and neutron. The first nuclear correction is expected to contribute at the few-percent level and comes with an undetermined low-energy constant. We discuss its relation to earlier potential-model calculations.