The broadband variability of many accreting systems displays characteristic structures; log-normal flux distributions, root-mean square (rms)-flux relations, and long inter-band lags. These characteristics are usually interpreted as inward propagating fluctuations of the mass accretion rate in an accretion disk driven by stochasticity of the angular momentum transport mechanism. We present the first analysis of propagating fluctuations in a longduration, high-resolution, global three-dimensional magnetohydrodynamic (MHD) simulation of a geometrically thin (h/r ≈ 0.1) accretion disk around a black hole. While the dynamical-timescale turbulent fluctuations in the Maxwell stresses are too rapid to drive radially coherent fluctuations in the accretion rate, we find that the lowfrequency quasi-periodic dynamo action introduces low-frequency fluctuations in the Maxwell stresses, which then drive the propagating fluctuations. Examining both the mass accretion rate and emission proxies, we recover lognormality, linear rms-flux relations, and radial coherence that would produce inter-band lags. Hence, we successfully relate and connect the phenomenology of propagating fluctuations to modern MHD accretion disk theory.