Marie Elisabeth Wilhelmine was born as the seventh child and fifth daughter of Charles Louis, Hereditary Prince of Baden and his wife, Landgravine Amalie of Hesse-Darmstadt.

Marie and her mother-in-law, Princess Augusta of Great Britain, came to see him at his sick-bed, but when the French army headed toward Hamburg, they were advised by the British ambassador to flee, and left shortly before his death.

Her brother, the Hereditary Prince of Baden, was married to Stephanie de Beauharnais, and an ally of Napoleon, and joined the emperor in Berlin at the same time.

She accepted the suggestion and travelled alone toward Berlin, but was stopped in Stralsund on the order of her husband,[2] as it was believed at the time that Napoleon had plans to marry her to his brother Jérôme Bonaparte.

She was reportedly used to an informal interaction with her ladies-in-waiting and felt restricted in the household of her strict and temperamental brother-in-law the king, with whom she found it difficult to get along.