The magmatically accreted oceanic crust contains two distinct layers, the upper and the lower crust, whereas the tectonically controlled crust may have gabbros and serpentinite close to the seafloor. Using full waveform inversion applied to ocean bottom seismometer data, we reveal the presence of a strong lateral variability in the 40 – 48 Ma old oceanic crust in the slow-spreading equatorial Atlantic. Over a 120 km-long section we observe four distinct 20-30 km long crustal segments. The segment affected by the St Paul FZ consists of three layers, 2 km thick layer with velocity <6 km/s, 1.5 km thick middle crust with velocity 6-6.5 km/s, and an underlying layer with velocity ~7 km/s in the lower crust. The segment associated with an abyssal hill morphology contains high velocity ~7 km/s from a shallow depth of 2 – 2.5 km below the basement, indicating the presence of either serpentinized peridotite or primitive gabbro close to the seafloor. The segment associated with a low basement morphology has 5.5 – 6 km/s velocity starting near the basement extending down to a depth of 4 km, indicating chemically distinct crust. The segment close to the Romanche transform fault, a normal oceanic crust with velocity 4.5-5 km/s near the seafloor indicates a magmatic origin. The four distinct crustal segments have a good correlation with the overlying seafloor morphology features. These observed strong crustal heterogeneities could result from alternate tectonic and magmatic processes along the ridge axis, possibly modulated by chemical variations in the mantle.