Pre-heated milk was gelled by acidification at 60, 70, 80, and 90 °C, to pH 5.2 or 4.6. The resultant milk gels were characterised in terms of composition, molecular protein bonds, and water mobility. The protein network structure of the gels was mainly governed by calcium bonds (30–63%), independent of the acidification temperature and pH. However, acidification temperature affected the aggregation kinetics and buffer capacity of the milk. Increased temperature led to an increase in total calcium in the gels (187% and 71% for pH 5.2 and 4.6 respectively) since colloidal calcium phosphate dissociated to a lesser degree, increasing the calcium bonds in the protein structure network. The largest water population in the gels was assigned to protons entrapped within the protein network, and the transverse relaxation time decreased with both increase in acidification temperature and decrease of pH, due to the increasing density of the gel aggregates.