Insulating quantum spin liquids can undergo a confinement transition to a valence bond solid via the condensation of topological excitations of the associated gauge theory. We extend the theory of such transitions to fractionalized Fermi liquids (FL∗): These are metallic doped spin liquids in which the Fermi surfaces only have gauge neutral quasiparticles. Using insights from a duality transform on a doped quantum dimer model for the U(1)-FL∗ state, we show that projective symmetry group of the theory of the topological excitations remains unmodified, but the Fermi surfaces can lead to additional frustrating interactions. We propose a theory for the confinement transition of Z2-FL∗ states via the condensation of visons. A variety of confining, incommensurate density wave states are possible, including some that are similar to the incommensurate d-form factor density wave order observed in several recent experiments on the cuprate superconductors. © 2016 American Physical Society.