In 1853 she traveled with her mother Ludovika and her younger sister Elisabeth to the resort of Bad Ischl, Upper Austria with the hopes that she would become the bride of their cousin Franz Josef, then the emperor of Austria. He decided that he preferred Elisabeth instead. Helene was unusually pious, and would have fit into the Habsburg court well. She had one quality, though, that would not have been accepted: she was habitually late for things. After the missed engagement she became depressed and Ludovika became concerned that Helene would take the veil and join a convent.
Helene had almost come to terms with remaining single. At 22 years old she was considered to be an "Old Maid," but her mother arranged for her to meet the rich hereditary prince Maximilian Anton Lamoral of Thurn and Taxis. Duke Max in Bavaria, Helene's father, invited the Thurn and Taxis family to Possenhofen for a hunting party. Prince Maximilian was immediately introduced to Helene.
While the prince was vacationing at Possenhofen, he brought his marriage plans to his parents, who immediately agreed. The only difficulty involved was that although the Thurn and Taxis family were counted among the richest in the land, they were not considered social equals for a princess of royal blood and a member of the House of Wittelsbach. Therefore, King Maximilian II of Bavaria did not agree to a marriage between the two, but through Elisabeth's influence on the king, the marriage took place nevertheless. The wedding ceremony was held on August 24, 1858 at Possenhofen. To mark the occasion, the in-laws gave the bride a necklace worth 160,000 Gulden. Helene is consider to have the only happy marriage among her siblings.
Her daughter Louisa was born in 1859, along with a second daughter Elisabeth in 1860. Shortly after the birth of her second child she traveled to Corfu to visit her sister Elisabeth, who was very ill. She returned by way of Vienna, where she reported to Franz Josef on the poor state of his wife.
She gave birth to a hoped-for son in 1862, named Maximilian, and in 1867 another son named Albert.
Even though the couple had a happy marriage, it was overshadowed by the severe illness of her husband Maximilian, who had chronic kidney disease. Neither a course of treatment in Karlsbad nor the best doctors could save him. He died in 1867 at the age of only 36 years.
Helene took her mind off her sorrows with charitable activities. She received guardianship of her children from the Austrian emperor. Her father-in-law began to include her in the business affairs of the House of Thurn and Taxis, so that he saw in her a support and successor. In this way she was the head of the family until her oldest son reached his majority.
In 1877 her youngest daughter Elisabeth married Prince Miguel of Braganza, the Miguelist claimant to the throne of Portugal. Elisabeth's health deteriorated after the birth of her first child, and she eventually died in 1881.
In 1879 Helen's oldest daughter Louisa married the young Prince Friedrich of Hohenzollern-Sigmaringen.
In 1883 her son Maximilian took over the leadership of the family business, but the well-trained young man fell ill. He suffered from severe heart attacks and died in 1885 of a pulmonary embolism. This left Helene the family head again, until 1888 when her son Albert reached his majority and took over the family businesses. As a result Helene retired and became absorbed in her beliefs.
She became very ill in 1890, and her sister Elisabeth hurried to her side. Elisabeth was the last person to speak with Helene. At her bedside Elisabeth opined, "We both have difficult times in our life." The dying Helene retorted, "Yes, but we had feelings." Helene died of a stomach disease.