Andy Pag, 34, from London, and 39-year-old John Grimshaw, from Poole, will drive more than 4,500 miles to Timbuktu, in Mali, in a bid to raise public awareness about biofuels and the role they can play in reducing the impact of climate change.
Their vehicles will run on a fuel created by Lancashire-based biodiesel producers Ecotech, who have developed a process to turn waste chocolate into car fuel.
The two men are to take a small processing unit with them on the trip, expected to take three weeks, to convert waste oil products into fuel.
They are taking 2,000 litres of bio-diesel made from 4,000 kilograms of chocolate misshapes, the equivalent of 80,000 chocolate bars, to fuel their adventure.
They will drive across France and Spain and then catch another ferry to Morocco, following which they will cross the country to Mauritania. From there, they will drive through the Sahara to Timbuktu.
To traverse the shifting desert sands and the pot-holed roads in Mali, Pag and Grimshaw will drive two converted 4x4 Toyota Land Cruisers, which are carried in the main lorry.
Timbuktu was picked as the destination because it is already feeling the effects of climate change, Pag said.
"Timbuktu is renowned as being the back of beyond, the furthest place away that you can possibly imagine. If we can make it there with biofuel, there is no reason why motorists can't use it on the school run or their commute to work," the Independent quoted him, as saying.
Pag said he hoped the trip would make more people realise that ordinary diesel cars can run on biodiesel without any adaptations.
"I have made many expeditions and visited these amazing landscapes but to get there I have contributed to their destruction by driving a guzzling diesel engine. I wanted to do something that is carbon neutral. What we have actually done is carbon negative," he said.
The pair will deliver a biodiesel processing unit to MFC, a Malian charity, which will allow biodiesel to be produced locally from used cooking oil.
Pag and Grimshaw hope to complete their journey shortly before Christmas and will remain in Mali for the festive season.