In 1669 John Charles bought the Fürstenhof of Gelnhausen, which included the Residenz, gardens and parcels of land that had first been granted by the Holy Roman Emperor to an earlier Wittelsbach, the Elector Palatine Louis III in 1435. In 1671 John Charles and his brother jointly inherited the county palatine of Birkenfeld. In 1673 they agreed that although Christian would keep Birkenfeld as well as another inheritance, Bischweiler, John Charles would receive the Neuburg appanage, a civil list of 6,000 florins constituting one-third of the revenues from yet another family estate, the county-palatine of Neuburg - plus annual delivery of four cart-loads of Moselle wine from the cellars of Trarbach. In compacts with his brother Christian II signed in 1681 and 1683, John Charles was deputised with the administration of Gelnhausen. John Charles married his first wife, Princess Sophie Amalie, in 1685 in Weikersheim. She was a daughter of Prince Frederick, Count Palatine of Zweibrücken and Countess Anna Juliane von Weikersheim, the widow of Count Siegfried of Hohenlohe-Weikersheim. Although Sophie Amalie died 30 November 1695 without having borne him a male heir, John Charles wrote Christian on 25 July 1696 declaring that if, feeling unable to continue living alone and heeding his heart's desire, he were to remarry it would only be a marriage of affection, since he was in no position to maintain a lady of rank. Three days later, he wed his late wife's lady-in-waiting, Esther Maria von :de:Witzleben |Witzleben-Elgersburg, the 30-year-old widow of a Herr von :de:Brömbsen|Brömbsen. Although her family belonged to the ancient Thuringian nobility they lacked the status of Imperial immediacy enjoyed by the Counts Palatine and Esther Maria's father, Georg Friedrich von Witzleben-Elgersburg, occupied the post of chief ranger at the minuscule court of the Duchy of Saxe-Römhild. Within weeks John Charles found himself trying to conciliate his disapproving brother, disclosing the marriage but assuring him that it was a strictly private arrangement, and that should any children be born thereof he "would claim no more for them than to be taken as nobles, so that there is nothing to fear with regard to the succession." By August Johann Carl had entered into an agreement to this effect with his older brother, but later changed his mind. He petitioned the Emperor to make his wife an Imperial countess, while Christian II refused to recognise the children born to his brother's marriage subsequently as agnates of the dynasty. John Charles died in 1704 and his widow filed a lawsuit against his brother in the Aulic Council of the Empire on 3 September 1708. She obtained, on 11 April 1715, full recognition for herself and her children as princely dynasts. Her brother-in-law Christian II acquiesced in an agreement of 29 October 1716, recognising her children's Palatine titles and succession rights, and increasing their allowance from 6,000 to 50,000 gulden. Nonetheless, other branches of the House of Wittelsbach continued to treat John Charles's children as morganatic, declining to acknowledge their eligibility to inherit the dynasty's patrimonies. In the Wittelsbach family compact of 1771 establishing reciprocal inheritance rights between the Palatine and Bavarian branches, heirs to their realms were restricted to agnates who were legitimate and "not born of unequal marriage". However the Peace of Teschen which concluded the War of the Bavarian Succession in 1779 finally recognised, in Article 8, the dynastic rights of the descendants of John Charles and Esther Marie von Witzleben, whose grandson, Wilhelm, received in 1803 the Duchy of Berg as an appanage from the Elector of Bavaria in compensation for the cession of his territories on the left bank of the Rhine to Napoleon. Berg was summarily re-allocated to Napoleon's brother-in-law, Joachim Murat, by Bavaria in 1806 in exchange for the Margraviate of Ansbach, but the title of Duke in Bavaria, granted by the Holy Roman Emperor to Count Palatine Wilhelm on 16 February 1799 continued to be borne by their direct descendants and recognised until abolition of the German Empire in 1918, and remains in use by their adopted descendants in the 21st century.
Issue
John Charles and Sophie Amalie of Zweibrücken had one daughter:
Juliane Magdalene
John Charles and Esther Maria von Witzleben had five children:
As a member of the House of Wittelsbach, he held the titles of Count Palatine of the Rhine, Duke in Bavaria, Count of Veldenz, Sponheim, Rappoltstein and Hohenack. As head of his own cadet branch of the dynasty, he was known as the Count Palatine of Birkenfeld at Gelnhausen. All of his dynastic male-line descendants have borne since 1799, as their primary title, "Duke or Duchess in Bavaria", embellished since 1845 with the style of Royal Highness.