During the past few years it has been reported that a thin AlN spacer of few nanometers needs to be inserted in InAlN/GaN high electron mobility transistors (HEMTs) to obtain high 2DEG carrier mobility. This work presents a systematic study of the effects of varying the ammonia flow in the AlN spacer of InAlN/AlN/GaN HEMTs grown by low pressure metalorganic vapour phase epitaxy (LP-MOVPE). The strain state, the surface roughness and the growth rate of AlN were found to be dependent on the V/III ratio. In addition the ammonia flow in the interlayer has a strong impact on the structural properties of the subsequent InAlN barrier layer and on the electrical properties of the structure. A sheet resistance as low as 327 Ω/□ with a sheet carrier density of 1.5 × 1013 cm−2 has been obtained at room temperature.