Württemberg lost around one third of its territory in 1629. Julius Frederick was removed as guardian in 1633 when Eberhard was declared of full age at which point he assumed full rule of the Duchy. Following a major defeat of Württemberg troops in the battle of Nördlingen on 6 September 1634, Württemberg was severely looted and plundered.
Eberhard fled to Strasbourg, where he married in 1637, returning to Württemberg in 1638 after long negotiations with Ferdinand III of the Holy Roman Empire. By this time many territories had already been passed on by the Emperor to other parties to push forward Catholicism in the region.
The Duchy of Württemberg was reinstated after long negotiations resulting in the Peace of Westphalia of 1648, despite or maybe because of the effects of war, poverty, hunger and the Bubonic plague all of which reduced the population from 350,000 in 1618 to 120,000 in 1648.
Eberhard III entered into an inheritance agreement with his younger brother Frederick thereby handing over ownership of the Duchy of Württemberg-Neuenstadt and thus establishing a new branch line of the duchy. In 1651, Eberhard came to a similar agreement with another brother, Ulrich affecting the Castle of Neuenbürg.
Dorothea Amalie of Württemberg-Stuttgart (13 February 1643 – 27 March 1650), died in childhood.
Christine Friederike of Württemberg-Stuttgart (28 February 1644 – 30 October 1674); married on 28 May 1665 to Prince Albert Ernest I of Oettingen-Oettingen and had issue, among which was the Duchess consort of Brunswick-Lüneburg.
Anna Katharine of Württemberg-Stuttgart (27 November 1648 – 10 November 1691).
Karl Christof of Württemberg-Stuttgart (28 January 1650 – 2 June 1650), died in infancy.
Eberhardine Katharine of Württemberg-Stuttgart (12 April 1651 – 19 August 1683); married on 30 April 1682 her brother in law, Prince Albert Ernest I of Oettingen-Oettingen.
Karl Maximilian of Württemberg-Stuttgart (28 September 1654 – 9 January 1689).
Secondly, he married on 20 July 1656 with Countess Marie Dorothea Sofie of Oettingen-Oettingen (29 December 1639 – 29 June 1698). They had eleven children, only four of whom lived to adulthood:
George Frederick of Württemberg-Stuttgart (24 September 1657 – 18 October 1685), killed in the Battle of Kassa against the Ottomans.
Stillborn son (12 April 1659).
Albrecht Christian of Württemberg-Stuttgart (13 June 1660 – 20 January 1663), died in childhood.
Louis of Württemberg-Stuttgart (14 August 1661 – 30 November 1698).
Joachim Ernst of Württemberg-Stuttgart (28 August 1662 – 16 February 1663), died in infancy.
Philipp Siegmund of Württemberg-Stuttgart (6 October 1663 – 23 July 1669), died in childhood.
Karl Ferdinand of Württemberg-Stuttgart (13 October 1667 – 13 June 1668), died in infancy.
John Frederick of Württemberg-Stuttgart (10 June 1669 – 15 October 1693), died in a duel with count János Pálffy near Herrenberg.