Suzanne had an elder brother named Charles who was born in 1476 and died unmarried in 1498. After this death, Suzanne's father grew concerned about the succession to the Bourbon lands. He had no surviving sons or brothers. By the Salic law which prevailed in France, his heir presumptive was Louis de Bourbon-Montpensier, head of the Montpensier family, a cadet branch of the Bourbons. Montpensier was Suzanne's second cousin as their grandfathers had been brothers.
The year 1498 was also that in which Anne's brother King Charles VIII died suddenly in an accident, leaving no sons or brothers. The succession of France itself was in controversy, because the nearest agnatic dynast, Louis XII was a distant second cousin once removed to Charles VII (and to Anne). Since Anne and Peter had served as Charles' co-regents, they held power which could make or mar the succession of Louis XII. They made a bargain with him: as the price of Bourbon support for his accession, Louis XII would have to recognize the seven-year-old Suzanne as her father's heiress to the Bourbon lands, and issue letters patent to that effect. Louis had little choice but to assent to this innovation, at least for the moment; the Salic law which precludes the succession of females was a cornerstone of French law and custom. Indeed, it was due to the Salic law that Louis rather than Anne had acceded to the throne of France.
In 1503, Peter died and Suzanne became duchess regnant. Her mother Anne became regent during Suzanne's minority.
As the agnatic heir to the Bourbon lands, Louis II, Count of Montpensier, was a suitable young man, and as marriage with him would avert a struggle for the succession (quite inevitable otherwise), Suzanne's parents initially groomed him as their future son-in-law, despite the concession they had extracted from Louis XII regarding the succession. However, the teenage Montpensier mortally offended Peter by condemning and denouncing the letters patent concerning the succession which Louis XII had issued, and asserting that succession to the Bourbon lands and titles was his own patrimony and birthright and not something he needed to thank his wife or her father for.
An enraged Peter decided to betroth Suzanne to Charles IV, Duke of Alençon, a great favourite of Louis XII, and therefore likely to be able to protect the duchy against both Bourbon-Montpensier challenges and royal encroachment. Anne was not in favour of this arrangement because of the political complications it would certainly cause, since Bourbon-Montpensier would definitely pursue his dynastic claim. However, Peter prevailed and the contract of betrothal was signed on 21 March 1501 at Moulins, Alençon being eleven years old and Suzanne nine.
Two years later, and before the wedding could be solemnised, Peter died of a fever. Incidentally, Louis of Montpensier had also died before this, and had been succeeded by his younger brother Charles III of Bourbon-Montpensier. With Peter and Louis both dead, the issues which had plagued their relationship could also be laid to rest. Anne broke off the arrangement with Alençon and arranged for Suzanne to marry the next Bourbon heir-male, Charles III, Duke of Bourbon, thereby averting a succession dispute over the Bourbon inheritance.
On 10 May 1505, at Château du Parc-les-Moulins, Suzanne was married to her second cousin Charles de Bourbon. Charles was immediately made co-ruler of the Bourbon lands. After the wedding, the duke and duchess of Bourbon made a tour through their domains along with Anne, something they would repeat many times during their reign.
It does not appear that Suzanne herself actually participated in state affairs: her spouse and her mother jointly managed the affairs of the Duchys and were described as good partners in administration and politics. Duchess Suzanne reportedly suffered from delicate health and was frequently described by chronicles as being of a ‘general disposition’ and having a ‘deformity’, though her condition is not described more closely.
An heir was born to Charles and Suzanne on 17 July 1517 and was baptised François in October 1517, in honour of Charles' good friend, King Francis I of France. The child was given the title Comte de Clermont. However, he died after living for only a few months. Later, Suzanne also gave birth to stillborn (or short-lived) twins.
Suzanne died at Château de Châtellerault in 1521. She was buried in Souvigny Priory, Souvigny. Her health had been frail throughout her last years. Her mother, who had always been fearful about her daughter's health, outlived her by one year. Suzanne's husband Charles kept his position as Duke of Bourbon after her death. He never remarried and died in 1527. Their death without heirs caused the lands of the Dukes of Bourbon to eventually be merged into the kingdom of France.
The death of Suzanne and Charles marked respectively the extinctions of the two senior-most branches of the Bourbon family, namely Suzanne's natal "Bourbon" branch and Charles' "Bourbon-Montpensier" branch. The agnatic heir to both was an extremely distant cousin, Charles, Duke of Vendôme, head of the "Bourbon-Vendome" branch, which came to be called simply "the House of Bourbon" because it was now the senior-most branch. Indeed, the Vendome branch was destined also to inherit the throne of France: Charles, Duke of Vendôme was the grandfather of Henry IV of France, the first "Bourbon" king of France.