We use thermochemical equilibrium calculations to model iron, magnesium, and silicon chemistry in the atmospheres of giant planets, brown dwarfs, extrasolar giant planets (EGPs), and low-mass stars. The behavior of individual Fe-, Mg-, and Si-bearing gases and condensates is determined as a function of temperature, pressure, and metallicity. Our results are thus independent of any particular model atmosphere. The condensation of Fe metal strongly affects iron chemistry by efficiently removing Fe-bearing species from the gas phase. Monatomic Fe is the most abundant Fe-bearing gas throughout the atmospheres of EGPs and L dwarfs and in the deep atmospheres of giant planets and T dwarfs. Mg- and Si-bearing gases are effectively removed from the atmosphere by forsterite (Mg2SiO4) and enstatite (MgSiO3) cloud formation. Monatomic Mg is the dominant magnesium gas throughout the atmospheres of EGPs and L dwarfs and in the deep atmospheres of giant planets and T dwarfs. Silicon monoxide (SiO) is the most abundant Si-bearing gas in the deep atmospheres of brown dwarfs and EGPs, whereas SiH4 is dominant in the deep atmosphere of Jupiter and other gas giant planets. Several other Fe-, Mg-, and Si-bearing gases become increasingly important with decreasing effective temperature. In principle, a number of Fe, Mg, and Si gases are potential tracers of weather or diagnostic of temperature in substellar atmospheres.