Northern Apulia has primary and secondary chert sources which were exploited in prehistory. During Neolithic period, on the north-eastern coast of the Gargano promontory, an important network of mines represented one of the most significant primary chert sources in the Adriatic area. However, easily accessible secondary chert sources are available in the Tavoliere plain in several synthems from the southern Appennines chain to the Gulf of Manfredonia. This work provides an overview of chert sources distributed in the Gargano and Tavoliere plain by means of a combination of up-to-date geological and archaeological information. Moreover, the lithic industries of eight Early and Middle Neolithic settlements were sampled in order to understand the procurement strategies of chert or tools used by communities settled in the Tavoliere plain. A non-destructive multi-parametric protocol for chert investigations (NM-PCI) method was applied to all the collected Gargano mines and secondary chert from the Tavoliere area. The results obtained demonstrate a high percentage of secondary chert used in the investigated sites, and the exploitation of mined chert essentially for the production of blades. In this latter case, provenance from the mines of Maiolica Fm is more frequent than that from mines of Peschici Fm. The polygenic nature of the pebbles occurring in the different synthems is the consequence of different sedimentary histories, as witnessed by the difference in the lithological array between inland and coastal synthems, and makes difficult any attribution to a specific source. If on the one hand these results further testify the circulation of mined Gargano chert in the Tavoliere plain in the Early Neolithic, on the other hand they demonstrate that the secondary coastal pebbles, especially those of southern Gargano lithotypes, were largely used, even in inland settlements. Moreover, these results suggest the exploitation of other primary cherts of the southern Gargano. This underlines the importance of further archaeological and geological investigations to better understand the exploitation and circulation of chert in Northern Apulia and in the Adriatic area.