EX Lup is a low-mass pre-main-sequence star that occasionally shows accretion-related outbursts. Here, we present JWST/MIRI medium-resolution spectroscopy obtained for EX Lup 14 yr after its powerful outburst. EX Lup is now in quiescence and displays a Class II spectrum. We detect a forest of emission lines from molecules previously identified in infrared spectra of classical T Tauri disks: H2O, OH, H2, HCN, C2H2, and CO2. The detection of organic molecules demonstrates that they are back after disappearing during the large outburst. Spectral lines from water and OH are for the first time deblended and will provide a much-improved characterization of their distribution and density in the inner disk. The spectrum also shows broad emission bands from warm, submicron-size amorphous silicate grains at 10 and 18 μm. During the outburst, in 2008, crystalline forsterite grains were annealed in the inner disk within 1 au, but their spectral signatures in the 10 μm silicate band later disappeared. With JWST we rediscovered these crystals via their 19.0, 20.0, and 23.5 μm emission, the strength of which implies that the particles are at ~3 au from the star. This suggests that crystalline grains formed in 2008 were transported outwards and now approach the water snowline, where they may be incorporated into planetesimals. Containing several key tracers of planetesimal and planet formation, EX Lup is an ideal laboratory to study the effects of variable luminosity on the planet-forming material and may provide an explanation for the observed high crystalline fraction in solar system comets.