The two giants of Spanish football meet again in their 236th competitive clash in just eight days time at the Bernabeau.
Manchester United boss Jose Mourinho was in charge of Real during the majority of Alonso's four year spell in the capital.
And the former Liverpool midfielder has revealed that the players used to have meetings about how to stop Messi's huge impact on Los Clasicos.
"Messi did me a lot of damage, I suffered a lot," he explained to Ecos del Balon.
"He made us squeeze our heads a lot. We spoke a lot with Mourinho and with Sergio [Ramos].
"How was he damaging us? How could we control him?
"Messi was playing, and behind him on the right of midfield was Xavi. And they provoked me."
"Xavi would show me the ball, I would go, Messi would get in behind me and Sergio would have to come out to cover him, and they cut through us.
Messi is the top scorer in the history of games between Barcelona and Real Madrid with a remarkable 24 goals.
Alonso explained that eventually they realised that Sergio Ramos couldn't handle marking the five time Ballon d'Or winner, so he took up the challenge.
"You only began to control Messi when it was me, not Sergio, who was in charge of marking him," he added.
"Xavi called me, but I stayed with Messi and Sergio did not have to come out, and from there, we controlled him pretty well.
"We sacrificed metres on the pitch, and to be able to win the ball back, to prioritise dealing with Messi.
"And when we controlled this position, the Barca-Madrid games became even."
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