The regulator ruled that Pepsico's Greek snack unit breached competition rules from 2000 to 2008.
"The Competition Commission... will not allow any kind of anti-competitive practices which shut out competitors and exploit consumers," the regulator's Chairman Dimitris Kiritsakis said in a statement.
Pepsico is the main rival of Greece's Coca-Cola Hellenic in the country's soft drinks and snack market.
Pepsico was not immediately reachable for comment.