The dramatic decay of dipole geomagnetic field intensity during the last 160 years coincides with changes in Southern Hemisphere (SH) field morphology and has motivated speculation of an impending reversal. Understanding these changes, however, has been limited by the lack of longer-term SH observations. Here we report the first archaeomagnetic curve from southern Africa (ca. 1000–1600 AD). Directions change relatively rapidly at ca. 1300 AD, whereas intensities drop sharply, at a rate greater than modern field changes in southern Africa, and to lower values. We propose that the recurrence of low field strengths reflects core flux expulsion promoted by the unusual core–mantle boundary (CMB) composition and structure beneath southern Africa defined by the African large low shear velocity province (LLSVP). Because the African LLSVP and CMB structure are ancient, this region may have been a steady site for flux expulsion, and triggering of geomagnetic reversals, for millions of years.