Intermediate-velocity clouds (IVCs) are HI halo clouds that are likely related to a Galactic fountain process. In-falling IVCs are candidates for the re-accretion of matter onto the Milky Way. Aims. We study the evolution of IVCs at the disk-halo interface, focussing on the transition from atomic to molecular IVCs. We compare an atomic IVC to a molecular IVC and characterise their structural differences in order to investigate how molecular IVCs form high above the Galactic plane. With high-resolution HI observations of the Westerbork Synthesis Radio Telescope and ^12^CO(1-0) and ^13^CO(1-0) observations with the IRAM 30m telescope, we analyse the small-scale structures within the two clouds. By correlating HI and far-infrared (FIR) dust continuum emission from the Planck satellite, the distribution of molecular hydrogen (H_2_) is estimated. We conduct a detailed comparison of the HI, FIR, and CO data and study variations of the XCO conversion factor. The atomic IVC does not disclose detectable CO emission. The atomic small-scale structure, as revealed by the high-resolution HI data, shows low peak HI column densities and low HI fluxes as compared to the molecular IVC. The molecular IVC exhibits a rich molecular structure and most of the CO emission is observed at the eastern edge of the cloud. There is observational evidence that the molecular IVC is in a transient and, thus, non- equilibrium phase. The average XCO factor is close to the canonical value of the Milky Way disk. We propose that the two IVCs represent different states in a gradual transition from atomic to molecular clouds. The molecular IVC appears to be more condensed allowing the formation of H_2_ and CO in shielded regions all over the cloud. Ram pressure may accumulate gas and thus facilitate the formation of H_2_. We show evidence that the atomic IVC will evolve also into a molecular IVC in a few Myr.