The Doldrums transform system, located in the Equatorial Atlantic at 7–8°N, is a 110 km-wide multi-fault shear zone, with five active transform faults separated by four short intra-transform ridge segments (ITRs). The two central ITRs, ITR-2 and ITR-3, are significantly deeper than the peripheral ridge segments, suggesting differences in the thermal conditions of the sub-ridge mantle. New chemical and radiogenic isotope data from on-axis lavas erupted across the transform domain reveal that the basalts from ITR-3 are enriched in alkalis (Na2O + K2O = 4.3 wt%; Na8 up to 3.7) and light rare earth elements (La/Sm)N = 0.86–0.97). However, these basalts have lower Sr and Pb isotope ratios than MORB from the Equatorial Atlantic (i.e., 87Sr/86Sr ∼ 0.70237 and 206Pb/204Pb ∼ 18), and relatively high Nd and Hf isotope ratios (143Nd/144Nd = 0.51315–0.51325; 176Hf/177Hf = 0.2832–0.28325). Hence, the mantle underlying ITR-3 is, on average, depleted in highly incompatible elements. Thermal models of the sub-ridge mantle show that it is also the coldest mantle region under the Doldrums system with the lowest crust production. Considering its location in the central transform domain, it is likely that the local mantle underwent melting beneath adjacent segments of the Mid-Atlantic Ridge (MAR) before remelting below ITR-3. We propose that the initial melting event beneath the MAR selectively removed the most fusible, geochemically enriched mantle components, leaving behind a predominantly peridotitic source, characterized by comparatively low Sr and Pb isotope ratios. Therefore, MORB from intra-transform ridge segments, such as those within the Doldrums transform system, provide a rare opportunity to constrain the isotopic composition of highly incompatible element depleted peridotitic mantle, which is a ubiquitous, but otherwise often camouflaged component of Earth’s mantle.