Electron cryomicroscopy (cryo-EM) allows high-resolution spatial visualization of biological specimens, however, it is challenging to chemically identify densities observed in cryo-EM. To overcome this, we combined cryo-EM with chemical imaging using focused ion beam secondary ion mass spectrometry (FIB-SIMS) for integrated spatio-chemical analysis. We illustrate the correlative workflow using multiple examples, demonstrating sub-cellular localisation of molecules inside small bacterial cells. We used our workflow to illuminate the mechanism of uptake of Bisphenol-AF pollutant molecules by environmental bacteria, yielding insights into the storage of these chemicals within cytosolic phase-separated aggregates. Given the versatility of the workflow, which is compatible with cryogenic optical microscopy and FIB-milled lamellae of multicellular specimens, cryo-EM-FIB-SIMS is an effective avenue to map elemental and molecular signatures in cryo-EM.