Police put the number of demonstrators at over 12,000, while organisers said 35,000 turned out.
While the “Grüne Woche” international agricultural fair was taking place in the German capital, the protesters took aim at government policy which prioritised large-scale farming, deemed damaging to health and the environment, to the detriment of small farmers and bio-growers.
“This protest… shows that the desire for a different agricultural policy is now undeniable,” said Green party co-leader Robert Habeck, who took part in Saturday's demonstration.
Conservative Agriculture Minister Julia Klöckner has received “an unequivocal message” from the street, said Saskia Richartz, spokeswoman for the protest organisers.
“We can't feed the whole world if we reduce industrial agricultural production,” the agriculture minister responded, while admitting that the sector needs to be “more efficient and respectful of the environment”.
More than 100 organisations took part in Saturday's colourful march, with 171 tractors descending on Berlin from several parts of the country.
The ministerial quarter around Brandenburg Gate remained partially blocked for several hours before the protest broke up peacefully.