This study represents results of first archaeo-geophysical prospection at the area of Kremenchuk Magnetic Anomaly (Poltava region, Ukraine). Pre-excavation magnetometer survey, electrical resistivity tomography (ERT) and ground-penetrating radar (GPR) measurements were performed on archaeological sites which are planned to be destroyed in near future due to development of iron ore quarries and construction of mine sites. Investigated archaeological monuments comprise settlements and burial mounds—kurgans—dated to Bronze and Early Iron Age occupying relatively high terrains in the floodplain of the Dnieper River. Based on prospection results of 18 sites and excavation of 6 ones, we evaluate the advantages and limitations of geophysical methods in confirming conclusions of visual archaeological inspection and targeting subsequent archaeological work. The recognised restrictions for geophysical methods are caused by high-gradient geomagnetic field, airborne magnetic pollution of soils and variable subsoil substrate—loess and sands. The magnetometer survey revealed an anomaly related to the remains of a large mound (the Bondari kurgan) against a background of high-gradient geomagnetic field. Large depression near the kurgan suggested its dating to the Bronze Age proved by subsequent archaeological excavations. The magnetic topsoil masks weak anomalies related to subsurface archaeological features and produces bright plough effects visible on the results of the magnetometer surveys. This is why, no anomalies sourced by mound of kurgan were recognised using this geophysical technique at the east from Gorishn’oplavnivskyi quarry. However, circular ditches and collapsed catacomb burials proved to cause detectable disturbance in the magnetic field. GPR measurements aided to identify the real diameter of kurgans by tracing the reflection associated with the mound-submound interface at sandy soil area. ERT results helped to clarify the structure of the large Novoselivska Mohyla kurgan. Two stages of construction were suggested from the two interpreted mounds of different resistivity. Smaller high resistivity anomalies are associated to primary and inserted burials. Magnetic anomalies caused by dwellings were found on the Bronze Age settlements as well as magnetic trace of shallow feature that was not identified during the archaeological excavations. The obtained results aid a proper understanding of the appearance of archaeo-geophysical anomalies and facilitate applying geophysical methods for archaeological needs in the region.