Earth’s magnetic field exhibits a dominant dipole morphology. Notwithstanding, significant deviations from the dipole are evident today, particularly the South Atlantic Anomaly (SAA), characterized by anomalously low-field intensity and high directional variability, diminishing the field’s shielding effect. To assess the persistence of SAA-like features over multimillion-year scales, we combine paleomagnetic data from Trindade Island (20°30’S, 29°22’W) with an evaluation of paleosecular variation (PSV) over the past 10 Myr. We employ synthetic models to explore how the position and intensity of magnetic flux patches at the core-mantle boundary can influence the long-term field behavior. Here we present results that reveal anomalous field signatures in the South Atlantic and the Atlantic-Pacific hemispheric asymmetries are enduring features, likely linked to a bottom-up control of PSV by the inner core’s heterogeneities but with contributions from mantle anomalies in the long-time range.