Johann Sebastian, 36, married the 20-year-old Anna Magdalena on 3 December of that year, seventeen months after the death of his first wife, Maria Barbara Bach.

In May 1723, the Bachs moved to Leipzig, where Johann Sebastian had been appointed Cantor of the Thomasschule and music director of the town.Anna Magdalena continued to sing professionally after her marriage.

Between 1723 and 1742, she gave birth to the following children: Christiana Sophia Henrietta (⁕spring 1723 †29 June 1726); Gottfried Heinrich (⁕26 February 1724 ⚰12 February 1763); Christian Gottlieb (〰14 April 1725 †21 September 1728); Elisabeth Juliana Friderica, called "Liesgen", who married Bach's pupil Johann Christoph Altnickol (〰5 April 1726 †24 August 1781); Ernestus Andreas (〰30 October 1727 †1 November 1727); Regina Johanna (〰10 October 1728 †25 April 1733); Christiana Benedicta (〰1 January 1730 †4 January 1730); Christiana Dorothea (〰18 March 1731 †31 August 1732); Johann Christoph Friedrich, called "Friedrich", the 'Bückeburg' Bach (⁕21 June 1732 †26 January 1795); Johann August Abraham (〰5 November 1733 †6 November 1733); Johann Christian, called "Christel", the 'London' Bach (⁕5 September 1735 – †1 January 1782); Johanna Carolina (〰30 October 1737 †18 August 1781) and Regina Susanna (〰22 February 1742 †14 December 1809)[6][7] As can be seen from the dates, seven of her 13 children died before reaching adulthood.

Only during the ten weeks from June to August 1732 were five of the couple’s children younger than 10 years of age living in the household.

[10] Together with her husband, Anna Magdalena Bach commanded a household to which not only the children belonged, but also private students and servants.

As a musician herself and the daughter of a court trumpeter, Anna Magdalena had the abilities and experience to monitor and participate in the activities.

In the case of the Bach family a committee of executors from Leipzig University ensured that these children were given their share of the inheritance.

During the distribution of the estate, she found herself in a position to cover the debts of her sister and paid the other heirs a sum equivalent to a year’s salary of a fully trained miner in Electoral Saxony.

[16] The widow Anna Magdalena took responsibility for her two youngest daughters, aged 8 and 12 years on their father’s death, and her 26-year-old mentally handicapped son Gottfried Heinrich.

[18] The only child that left home was Johann Christian who moved to his half-brother Carl Philipp Emanuel in Berlin for his further education.

[22] Recently, it has been suggested that Anna Magdalena Bach composed several musical pieces bearing her husband's name: Professor Martin Jarvis of the School of Music at Charles Darwin University in Darwin, Australia, claims that she composed the famed six cello suites (BWV 1007–1012) and was involved with the composition of the aria from the Goldberg Variations (BWV 988) and the opening prelude of The Well-Tempered Clavier.

[25]Writing in The Guardian, cellist Steven Isserlis said, "I'm afraid that his theory is pure rubbish," and continued, "How can anybody take this shoddy material seriously?"