At the age of thirteen, she was married to Louis Armand de Bourbon, Prince of Conti and as such was the Princess of Conti by marriage. Her father's favourite daughter, Marie Anne was widowed in 1685 aged 19.
On 16 January 1680, Marie Anne married her cousin, Louis Armand de Bourbon, Prince of Conti, in the chapel of the Château de Saint-Germain-en-Laye. He had fallen in love with her at first sight. Her dowry was one million livres. The marriage was the first between a Prince of the Blood and one of Louis XIV's legitimised daughters which caused a scandal at the time. After a disastrous wedding night, the marriage remained sterile and Marie Anne shocked the court when she openly stated that her husband was not good at making love.
In 1683, she lost her beloved brother the Count of Vermandois, who shared the same birthday with her. The young count had been exiled from court after being involved in a homosexual scandal involving the Chevalier de Lorraine, himself the long term lover of Marie Anne's uncle the Duke of Orléans. From all sources, Marie Anne was quite upset by her brother's death, while, according to contemporary accounts, the young man's parents did not even shed a tear.
In 1685, her husband contracted smallpox from Marie Anne. Although she recovered, he succumbed after five days. After his death, she was called Madame la Princesse Douairière, and also la Grande Princesse de Conti. She never remarried and even refused an offer of marriage from the Sultan of Morocco, Ismail Ibn Sharif preferring to be free.
During the five years of her marriage to the Prince of Conti, a Prince of the Blood, she was one of the most important ladies at her father's court.