Geochemical, mineralogical, micromorphological, microbiological, hydrochemical and hydrological joint investigations were performed at two coniferous podzolic sites in the north of Sweden and at one in the south of Finland. Mycorrhizal fungi were found to create numerous pores (3–10-μm diameter) in many weatherable mineral grains in the eluvial (E) horizon. During the growing season, identified low molecular weight (LMW) organic acids such as citric, shikimic, oxalic and fumaric acids comprised 0.5–5% of the DOC and 0.5–15% of the total acidity in soil solutions. Between 20% and 40% of the dissolved Al was bound to the identified LMW organic acids. Mineral dissolution via complexing LMW acids, probably exuded in part by the mycorrhiza hyphae, is likely to be a major weathering process in podzols. We found no evidence for a decreasing C/metal ratio of the migrating organo-metal complexes that could explain the precipitation of secondary Fe and Al in the illuvial (B) horizon. Instead, microbial degradation of organic ligands resulting in the release of ionic Al and Fe to the soil solution may be an important process facilitating the formation of solid Al–Si–OH and Fe–OH phases in the podzol B horizon. However, within the B horizon transport as proto-imogilite (PI) sols might be possible. In the B horizon, the extractable Al and Fe was predominantly inorganic. The large specific surface area (SSA) removable by oxalate extraction, the high point of zero charge salt effect (PZSE), the low cation exchange capacity (CEC) and the high sulphate exchange capacity (SEC), pointed to the presence of short-range ordered variable charge phases. Imogolite type material (ITM) was indeed identified in all B horizons by IR spectroscopy and crystalline imogolite was found in the deep B horizon of one profile. Mössbauer spectroscopy indicated that Fe in the form of ferrihydrite was formed by intergrowth with an Al–Si–OH phase. The high amounts of Fe and Al transported from the O to the E horizon indicate that there could be an upward transport of these elements before they are leached to the B horizon. We hypothesize that the LMW Al complexes are transported by hyphae to the mor (O) layer, partly released and subsequently complexed by high molecular weight (HMW) acids.