Assembly polls are due early next year in the hill state, where beef is a staple.
"I have decided to quit the party because I am a Christian and Garo first," Mr Marak said today, adding, "The BJP is hurting the sentiments here on the beef issue. Tribal society has its own laws. The BJP is trying to push Hindutva."
Mr Marak's cheaper beef offer earlier this week discomfited the party as its government at the Centre faced criticism about its new cattle trade rules. The state BJP distanced itself from Mr Marak's comments, calling those his own views. Meghalaya BJP chief Shibun Lyndoh said the party "is not against people having beef".
"Total beef ban is something that even people here do not support," he said, adding what was required in the state were regulations and hygienic slaughter houses.
The BJP is yet to comment on the exit of the leader, who commands a chunk of the tribal votes.
"Bernard is right to the extent that there are people in the BJP in Meghalaya who eat beef... In Meghalaya it is not the BJP's agenda to put a beef ban," said senior BJP leader Nalin Kohli. But he denied that the party will push for cheaper beef if it comes to power. "It is not the BJP's agenda to run markets that sale beef. That is for the market to decide. What Bernard says is his personal view not the party's view. "
The new cattle trade rule of the Centre, that has triggered widespread protests in Kerala, Karnataka and Tamil Nadu, says cattle sold in animal markers cannot be used for slaughter. After Kerala and West Bengal, Tripura's Left government has said it will not implement the rule, describing it as "anti-people".