And now years later, one of those notebooks has been translated by his son into "Whispers of War", a heart- wrenching tale of freedom and hope.
"Whispers of War: An Afghan Freedom Fighter's Account of the Soviet Invasion" by Khalili, Ambassador of Afghanistan to Spain and son of great Afghan poet Ustad Khalilullah Khalili, is published by Sage Books.
In letters to his wife Sohaillah, he writes of his journey through the Himalayan range, accompanied by a team of foreign journalists.
The book is an account of the search for ever elusive peace in a country ravaged by war - a war that changed the landscape of the country and the fabric of its society.
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"In my 13 trips into Afghanistan over the course of the whole jihad, I travelled to every corner and in each one, I had one thing always with me and that was my notebook to my wife. One of those notebooks is the one that my son translated and we made into 'Whispers of War'," he says.
"But more than the story of that young political officer, it is the story of the tears, pain, and suffering of the common people of that poor, war-torn country," Khalili told PTI.
He says he would write to his wife almost every hour.
"Whenever we took a break to try and regain some energy in order to keep going on, I would take out my notebook," he says, adding his notebooks helped him with that mental strength.
The inspiration for writing diaries came to him from love of his family and even more so the love for his nation.
He wrote over 40 notebooks, some political, some military and the others for his wife.
"My son, Mahmud, who translated 'Whispers of War' has plans to translate one more of my notebooks. This one is the trip to Herat. It is a totally different kind of feeling because I travel through the Southern provinces of Afghanistan, which has a different people and culture than people of the North," Khalili says.
He then recalls one such story when he saw a Nooristani woman extending her hand as if she was seeking alms.
"It was strange to me to see a woman begging in Nooristan. It was very unusual. They are poor but not beggars. I moved past quickly," he says.
"At that moment, one of the men said loudly, 'Khalili Sahib, she has something for you.' As I turned back, I saw that the woman instantly covered her face with her old black headscarf and kept one hand extended towards me.
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