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Abstract The poor thermal stability of lactoferrin (LF) hinders its bioavailability and use in commercial food products. To preserve LF from thermal denaturation, complexation with other biopolymers has been studied. Here we present the complex formation conditions, structural stability, and functional protection of LF by α‐lactalbumin (α‐LA). The formation of the LF–α‐LA complexes was dependent on pH, mass ratio, and ionic strength. Changing the formation conditions and cross‐linking by transglutaminase impacted the turbidity, particle size, and zeta‐potential of the resulting complexes. Electrophoresis, Fourier‐transform infrared spectroscopy, and circular dichroism measurements suggest that the secondary structure of LF in the LF–α‐LA complex was maintained after complexation and subsequent thermal treatments. At pH 7, the LF–α‐LA complex protected LF from thermal aggregation and denaturation, and the LF retained its functional and structural properties, including antibacterial capacity of LF after thermal treatments. The improved thermal stability and functional properties of LF in the LF–α‐LA complex are of interest to the food industry.