When war broke out in 1899, Duquesne returned to South Africa to join the Boer commandos as a lieutenant attached to the staff of Commandant General Piet Joubert in Pretoria.
He was wounded with a bullet through his right shoulder at the Siege of Ladysmith and promoted to the rank of captain in the artillery.
Duquesne was captured by the British at the Battle of Colenso, but escaped in Durban.

When the British forces began their offensive against Pretoria, some of the gold from the central bank was sent by train to the small town of Machadodorp and then by road to the neutral harbor of Lourenço Marques in Portuguese East Africa (now Maputo, Mozambique) to be shipped to the Netherlands for the use of  President Paul Kruger and other Boer exiles fleeing the Transvaal.
A final tally showed that about 1.5 million pounds (680,000 kilos) of gold bullion was removed from the South African Mint and National Bank between 29 May and 4 June 1900.
Duquesne was in command of one of these large shipments of gold that was sent by wagon; however, this gold never made it to its destination.
While in the bushveld of Portuguese East Africa, a violent disagreement broke out among the Boers.
When the struggle ended, only two wounded Boers, Duquesne, and the tottys (native porters) remained alive.
Duquesne ordered the tottys to hide the gold in the Caves of Leopards for safekeeping, to burn the wagons, and to kill the wounded.
He gave the tottys all the oxen, except for one which he rode away.
Historian Art Ronnie writes in 1995 that the buried central bank gold, commonly referred to as "Kruger's Millions" is only a legend; however, in more recent times there have been reports about discoveries in South Africa of the missing gold buried by Duquesne.

Duquesne joined the Boer forces again for the Battle of Bergendal, but his unit had to fall back to Portuguese East Africa where all were captured by the Portuguese and sent to an internment camp in Caldas da Rainha near Lisbon.
For Duquesne, this would become the watershed event, as Ronnie states, "life would never again be the same for him  ... In a few months he would be launched on a forty-year career as a professional spy and counterfeit hero – a man who would constantly reinvent himself to suit the needs of the moment."

At the internment camp in Portugal, he charmed the daughter of one of the guards, who then helped him escape to Paris.
From there, he made his way to Aldershot in England.
He then infiltrated the British army and was posted to wartime South Africa in 1901 as an officer.
He passed with troops through his parents' farm in Nylstroom, finding it to have been destroyed under Kitchener's scorched earth policy.
He also learned his sister had been raped and killed and his mother was dying in a British concentration camp.
As Ronnie states, "the fate of his country and of his family would breed in him an all-consuming hatred of England" and "would turn him into what (Duquesne biographer) Clement Wood called: a walking living breathing searing killing destroying torch of hate."

As a British officer, Duquesne returned to Cape Town with secret plans to sabotage strategic British installations and to kill Kitchener.
 He recruited 20 Boer men, but was betrayed by the wife of one.
On 11 October 1901, while attending a dinner for Sir Walter Hely-Hutchinson, the Cape Colony governor, he was arrested in full dress uniform for "conspiracy against the British government and on (the charge of) espionage."
He was court-martialled as a lieutenant in the British army and sentenced to be shot along with his co-conspirators.
The other 20 members of his team were executed by firing squad the next day, but as a plea-bargain his sentence was reduced to life in prison and in exchange Duquesne agreed to divulge secret Boer codes and to translate several Boer dispatches.
According to Ronnie, "for the rest of his life he swore he never betrayed the Boer cause but actually created new codes that would mislead the British."

He was imprisoned in Cape Town in the Castle of Good Hope, a fortification built by the
When war broke out in 1899, Duquesne returned to South Africa to join the Boer commandos as a lieutenant attached to the staff of Commandant General Piet Joubert in Pretoria. He was wounded with a bullet through his right shoulder at the Siege of Ladysmith and promoted to the rank of captain in the artillery. Duquesne was captured by the British at the Battle of Colenso, but escaped in Durban.
When the British forces began their offensive against Pretoria, some of the gold from the central bank was sent by train to the small town of Machadodorp and then by road to the neutral harbor of Lourenço Marques in Portuguese East Africa (now Maputo, Mozambique) to be shipped to the Netherlands for the use of  President Paul Kruger and other Boer exiles fleeing the Transvaal. A final tally showed that about 1.5 million pounds (680,000 kilos) of gold bullion was removed from the South African Mint and National Bank between 29 May and 4 June 1900. Duquesne was in command of one of these large shipments of gold that was sent by wagon; however, this gold never made it to its destination. While in the bushveld of Portuguese East Africa, a violent disagreement broke out among the Boers. When the struggle ended, only two wounded Boers, Duquesne, and the tottys (native porters) remained alive. Duquesne ordered the tottys to hide the gold in the Caves of Leopards for safekeeping, to burn the wagons, and to kill the wounded. He gave the tottys all the oxen, except for one which he rode away. Historian Art Ronnie writes in 1995 that the buried central bank gold, commonly referred to as "Kruger's Millions" is only a legend; however, in more recent times there have been reports about discoveries in South Africa of the missing gold buried by Duquesne.
Duquesne joined the Boer forces again for the Battle of Bergendal, but his unit had to fall back to Portuguese East Africa where all were captured by the Portuguese and sent to an internment camp in Caldas da Rainha near Lisbon. For Duquesne, this would become the watershed event, as Ronnie states, "life would never again be the same for him  ... In a few months he would be launched on a forty-year career as a professional spy and counterfeit hero – a man who would constantly reinvent himself to suit the needs of the moment."
At the internment camp in Portugal, he charmed the daughter of one of the guards, who then helped him escape to Paris. From there, he made his way to Aldershot in England. He then infiltrated the British army and was posted to wartime South Africa in 1901 as an officer. He passed with troops through his parents' farm in Nylstroom, finding it to have been destroyed under Kitchener's scorched earth policy. He also learned his sister had been raped and killed and his mother was dying in a British concentration camp. As Ronnie states, "the fate of his country and of his family would breed in him an all-consuming hatred of England" and "would turn him into what (Duquesne biographer) Clement Wood called: a walking living breathing searing killing destroying torch of hate."
As a British officer, Duquesne returned to Cape Town with secret plans to sabotage strategic British installations and to kill Kitchener.  He recruited 20 Boer men, but was betrayed by the wife of one. On 11 October 1901, while attending a dinner for Sir Walter Hely-Hutchinson, the Cape Colony governor, he was arrested in full dress uniform for "conspiracy against the British government and on (the charge of) espionage." He was court-martialled as a lieutenant in the British army and sentenced to be shot along with his co-conspirators. The other 20 members of his team were executed by firing squad the next day, but as a plea-bargain his sentence was reduced to life in prison and in exchange Duquesne agreed to divulge secret Boer codes and to translate several Boer dispatches. According to Ronnie, "for the rest of his life he swore he never betrayed the Boer cause but actually created new codes that would mislead the British."
He was imprisoned in Cape Town in the Castle of Good Hope, a fortification built by the 
Fritz Joubert Duquesne