Observables which distinguish boosted topologies from QCD jets are playing an increasingly important role at the Large Hadron Collider (LHC). These observables are often used in conjunction with jet grooming algorithms, which reduce contamination from both theoretical and experimental sources. In this paper we derive factorization formulae for groomed multi-prong substructure observables, focusing in particular on the groomed $D_2$ observable, which is used to identify boosted hadronic decays of electroweak bosons at the LHC. Our factorization formulae allow systematically improvable calculations of the perturbative $D_2$ distribution and the resummation of logarithmically enhanced terms in all regions of phase space using renormalization group evolution. They include a novel factorization for the production of a soft subjet in the presence of a grooming algorithm, in which clustering effects enter directly into the hard matching. We use these factorization formulae to draw robust conclusions of experimental relevance regarding the universality of the $D_2$ distribution in both $e^+e^-$ and $pp$ collisions. In particular, we show that the only process dependence is carried by the relative quark vs. gluon jet fraction in the sample, no non-global logarithms from event-wide correlations are present in the distribution, hadronization corrections are controlled by the perturbative mass of the jet, and all global color correlations are completely removed by grooming, making groomed $D_2$ a theoretically clean QCD observable even in the LHC environment. We compute all ingredients to one-loop accuracy, and present numerical results at next-to-leading logarithmic accuracy for $e^+e^-$ collisions, comparing with parton shower Monte Carlo simulations. Results for $pp$ collisions, as relevant for phenomenology at the LHC, are presented in a companion paper.
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