Velez's resignation followed a recent coffee congress in Colombia during which he presented historic results that saw crops valued at 14.5 trillion pesos ($3.03 billion) and exports worth more than $3.74 billion.
"This decision to step aside opens a space so that, in harmony with the current government, the federation can continue working for the well-being of the 540,000 coffee-growing families in the country," Velez said in a statement.
He did not give reasons for his resignation.
Velez's resignation will be followed by an orderly succession process, he said, during which the national congress of coffee growers will elect a new federation head in the coming months.
Colombia is the leading supplier of washed arabica coffee. The federation sees production reaching almost 12 million 60-kg (132-lb.) bags in 2022.
In early October, an industry leader told Reuters that Colombia's coffee production this year is set to fall to an eight-year low, with a drop in plantation renovations and in the use of fertilisers storing up problems for future crops.
Elsewhere, Brazilian coffee farmers and experts have downgraded expectations regarding next year's crop in the world's largest producer after a mostly negative post-flowering evolution in many of the areas they oversee.
According to them, initial expectations for an increase in production next year now look dim, with views converging for a crop that would be similar in size to the one harvested this year.