Common modal decomposition techniques for flow-field analysis, data-driven modelling and flow control, such as proper orthogonal decomposition and dynamic mode decomposition, are usually performed in an Eulerian (fixed) frame of reference with snapshots from measurements or evolution equations. The Eulerian description poses some difficulties, however, when the domain or the mesh deforms with time as, for example, in fluid–structure interactions. For such cases, we first formulate a Lagrangian modal analysis (LMA) ansatz by a posteriori transforming the Eulerian flow fields into Lagrangian flow maps through an orientation and measure-preserving domain diffeomorphism. The development is then verified for Lagrangian variants of proper orthogonal decomposition and dynamic mode decomposition using direct numerical simulations of two canonical flow configurations at Mach 0.5, i.e. the lid-driven cavity and flow past a cylinder, representing internal and external flows, respectively, at pre- and post-bifurcation Reynolds numbers. The LMA is demonstrated for several situations encompassing unsteady flow without and with boundary and mesh deformation as well as non-uniform base flows that are steady in Eulerian but not in Lagrangian frames. We show that application of LMA to steady non-uniform base flow yields insights into flow stability and post-bifurcation dynamics. LMA naturally leads to Lagrangian coherent flow structures and connections with finite-time Lyapunov exponents. We examine the mathematical link between finite-time Lyapunov exponents and LMA by considering a double-gyre flow pattern. Dynamically important flow features in the Lagrangian sense are recovered by performing LMA with forward and backward (adjoint) time procedures.