The normalcy of their family life was interrupted when Napoleon invaded Spain. Joachima had to flee with the children; Theodore, remaining behind, died. Though Joachima reexperienced a desire to enter a religious community, she attended to her duties as a mother. At the same time, the young widow led a life of austerity and chose to wear the habit of the Third Order of St. Francis as her ordinary dress. She spent much time in prayer and visiting the sick.
Four years later, with some of her children now married and younger ones under their care, Joachima confessed her desire to a priest to join a religious order. With his encouragement she established the Carmelite Sisters of Charity. In the midst of the fratricidal wars occurring at the time, Joachima was briefly imprisoned and, later, exiled to France for several years.
Sickness ultimately compelled her to resign as superior of her order. Over the next four years she slowly succumbed to paralysis, which caused her to die by inches. At her death in 1854 at the age of 71, Joachima was known and admired for her high degree of prayer, deep trust in God and selfless charity.