Only in the last decade have archaeologists working on Iroquoian sites in Ontario, Québec, and New York State begun to seize upon the potential of geophysical prospection and soil chemistry for identifying settlement features. Recent studies employing magnetic gradiometry, magnetic susceptibility, and soil phosphate analysis demonstrate that multi-method approaches have the potential to overcome the limitations imposed by intrusive historic features, soil composition, and underlying geology. We consider how specific aspects of the Iroquoian built environment, such as longhouses, palisades, and middens, might be visible in datasets produced by magnetic gradiometry, magnetic susceptibility, and soil phosphate analyses and apply these methods to two Iroquoian sites: Trent-Foster (BcGr-5), a late 16th-century Wendat village and Hamilton-Lougheed (BbHa-10), an early-to-mid 17th-century Tionontate village. At Trent-Foster, we interpret certain anomalies as potential longhouses, but suggest that a band of low magnetism cutting through the site may be due to underlying geology. At Hamilton-Lougheed, we identify a potential palisade and a likely habitation area. We conclude by acknowledging that the biggest imperative moving forward is the need for more ground-truthing to verify the presence or absence of built environment features suggested by geophysical and soil chemistry methods. We advocate for continued use and development of geophysical and geochemical methods on Iroquoian sites, particularly in the cultural resource management context, as they strike an important balance between preserving archaeological heritage and learning from that which is preserved, issues that are of the utmost importance to descendant communities and First Nations research partners.