Milk (MP) and whey (WP) ultrafiltration permeates were obtained from different dairy processing plants. The effects of pH (4 or 6) and heat treatments (63 °C, 30 min; or 110 °C, 6 min) on permeate stability were measured by the increase of turbidity, and precipitation of nitrogen and calcium. The antioxidant activity and the production of volatiles compounds, as affected by heat treatments, was also evaluated. WP showed a higher sensitivity to heat treatments than MP. Increasing heating temperature reduced the stability of permeates, with an intensified effect at pH 6. Calcium precipitation was the main factor responsible for the increase in turbidity. Lowering the pH to 4 prior to heating strongly limited the development of turbidity. Sterilisation improved antioxidant activity of both permeates, with a greater effect on WP. Sterilisation had no effect on the concentration of volatile aldehydes but promoted the formation of volatile sulfur compounds, and more significantly in WP.