Multi-sensor prospecting is a fast-emerging paradigm in archaeological geophysics. Given suitable ground conditions for navigation, sensor arrays drastically increase efficiency in data collection. In particular, geomagnetic prospecting benefits from this development. Despite these advancements, data processing still lacks a best-practice approach. Conventional processing methods developed for gridded data has been challenged by sensor arrays “roaming” in the landscape. In realization of the issue, the Innovative Geophysical Approaches for the Study of Early Agricultural Villages of Neolithic Thessaly (IGEAN) Project explored various innovative techniques for the betterment of the multi-sensor geomagnetic data processing. As a result, a modular pipeline is produced with minimal user intervention. In addition to standard steps, such as data clipping, various other algorithms have been introduced. This pipeline is tested over 20 Neolithic settlements in Thessaly, Greece, three of which are presented here in detail. The proposed workflow provides drastic improvements over raw data. As a result of these improvements, the IGEAN project revealed astonishing details on architectural elements, settlement enclosures, and paleolandscapes, changing completely the existing perspective of the Neolithic habitation in Thessaly.