The Úrkút manganese ore deposit (Transdanubian Range, Hungary) is one of the largest manganese accumulations to be formed during the Toarcian Oceanic Anoxic Event. In the past 60 years, the area was investigated intensively. The core storage facility of the manganese mine had more than 20,000 sample pieces. Most of these samples have never been investigated. During this study, which is the first widespread clay mineral study in the footwall of the Úrkút manganese ore deposit, we investigated 40 samples from seven boreholes (footwall rocks, black/gray shales below and above the first ore bed, and manganese carbonate ores). Although previous studies assumed that smectite is associated only with the ore beds, our research revealed its appearance in the footwall (Pliensbachian) as well. Simultaneously, tripoli (the local name of completely bleached chert) can also be found in the footwall. Based on the investigated samples, a sharp geochemical difference was detected between Pliensbachian and Toarcian sediments. In this paper, we try to trace the relationship between the smectite content of the footwall and the ore bed and compare these results with the observed geochemical changes. Based on the new data, we assume that the ore accumulation was caused by a flow system (upwelling-controlled ore formation).