Abstract Flat-spectrum radio quasars (FSRQs) are the most luminous blazars at GeV energies but only rarely emit detectable fluxes of TeV gamma rays, typically during bright GeV flares. We explore the gamma-ray variability and spectral characteristics of three FSRQs that have been observed at GeV and TeV energies by Fermi-LAT and VERITAS, making use of almost 100 hr of VERITAS observations spread over 10 yr: 3C 279, PKS 1222+216, and Ton 599. We explain the GeV flux distributions of the sources in terms of a model derived from a stochastic differential equation describing fluctuations in the magnetic field in the accretion disk and estimate the timescales of magnetic flux accumulation and stochastic instabilities in their accretion disks. We identify distinct flares using a procedure based on Bayesian blocks and analyze their daily and subdaily variability and gamma-ray energy spectra. Using observations from VERITAS, as well as Fermi, Swift, and the Steward Observatory, we model the broadband spectral energy distributions of PKS 1222+216 and Ton 599 during very high energy (VHE)–detected flares in 2014 and 2017, respectively, strongly constraining the jet Doppler factors and gamma-ray emission region locations during these events. Finally, we place theoretical constraints on the potential production of PeV-scale neutrinos during these VHE flares.