Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pH(i)) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical alpha alpha -hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pH(i) and the rate of pH(i) recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins. Hendus-Altenburger et al. provide biochemical, structural and functional information on the lipid interaction domain (LID) of the Na+/H+ Exchanger 1 (NHE1). They find that NHE1-LID is intrinsically disordered, but, when allowed to interact with a lipid membrane, forms a helical alpha alpha -hairpin, stabilized by hydrophobic and electrostatic interactions. This co-structure is fundamental for NHE1 activity, giving insight into membrane protein regulation via disordered domains.