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Negative stable carbon isotopic excursions have been observed throughout most of the mid‐depth (~1000–3000 m) Atlantic Ocean during Heinrich Stadial 1 (HS1) and the Younger Dryas (YD). Although there is an agreement that these mid‐depth excursions were in some way associated with a slowdown of the Atlantic Meridional Overturning Circulation (AMOC), there is still no consensus on the precise mechanism(s). Here we present benthic stable carbon and oxygen isotopic (δ13C and δ18O) records from five cores from the western equatorial Atlantic (WEA). Together with published benthic isotopic records from nearby cores, we produced a WEA depth transect (~800–2500 m). We compare HS1 and YD data from this transect with data from previously published North and South Atlantic cores and demonstrate that the largest negative δ13C excursions occurred in the WEA during these times. Moreover, our benthic δ18O records require the presence of two water masses flowing from the Southern Ocean, bisected by a Northern Component Water (NCW). Given that δ18O is a conservative water mass tracer, we suggest that δ13C was decoupled from water mass composition and does not correspond to simple alternations between northern and southern sourced waters. Instead, δ13C behaved non‐conservatively during HS1 and the YD. Consistently with our new 231Pa/230Th record from the WEA transect, that allowed the reconstruction of AMOC strength, we hypothesize that the negative δ13C excursions reflect an increase in the residence time of NCW in response to a weakened AMOC, allowing for a marked accumulation of 13C‐depleted respired carbon at the mid‐depth WEA.