Previous explorations of the Asymptotic Safety scenario in Quantum Einstein Gravity (QEG) by means of the effective average action and its associated functional renormalization group (RG) equation assumed spacetime manifolds which have no boundaries. Here we take a first step towards a generalization for non-trivial boundaries, restricting ourselves to action functionals which are at most of second order in the derivatives acting on the metric. We analyze two examples of truncated actions with running boundary terms: full fledged QEG within the single-metric Einstein-Hilbert (EH) truncation, augmented by a scale dependent Gibbons-Hawking (GH) surface term, and a bi-metric truncation for gravity coupled to scalar matter fields. The latter contains 17 running couplings, related to both bulk and boundary terms, whose beta-functions are computed in the induced gravity approximation. We find that the bulk and the boundary Newton constant, pertaining to the EH and GH term, respectively, show opposite RG running; proposing a scale dependent variant of the ADM mass we argue that the running of both couplings is consistent with gravitational anti-screening. We describe a simple device for counting the number of field modes integrated out between the infrared cutoff scale and the ultraviolet. This method makes it manifest that, in an asymptotically safe theory, there are effectively no field modes integrated out while the RG trajectory stays in the scaling regime of the underlying fixed point. As an application, we investigate how the semiclassical theory of Black Hole Thermodynamics gets modified by quantum gravity effects and compare the new picture to older work on `RG-improved black holes' which incorporated the running of the bulk Newton constant only. We find, for instance, that the black hole's entropy vanishes and its specific heat capacity turns positive at Planckian scales.