Franz Ferdinand appears to have first met Sophie Chotek in 1888 at a dance soirée in Prague where he was then stationed. Sophie was lady-in-waiting to Erzherzogin Isabella, a Princess of Cröy-Dülmen, who in 1878 had married Erzherzog Ferdinand von Habsburg-Toscana, Third Duke of Teschen, the wealthiest of all the Habsburgs, and by whom she had produced six daughters. A formidable woman of known matchmaking propensity, Isabella had designs on the Heir Apparent, to wit her eldest daughter Maria Christina – one of the Piperl. At first Franz Ferdinand and Sophie may have held just a mutual fondness for each other, but they kept this from just about everyone. However, upon Franz Ferdinand's return from Egypt – fully recovered – any fondness there may have been then blossomed into full-blown love ... which, even more so, had to be kept secret 'for the time being.' A scandal was waiting to break.

And break it did, albeit accidentally – although there are no documents to confirm the following 'legend.' In November 1898, during another of Franz Ferdinand's visits to Archduke Ferdinand and Isabella's home at Preßburg/Bratislava, he uncharacteristically allowed a 'security breach' to occur: he forgetfully left behind a personal pocket-watch at one of the stately home's tennis courts. A servant happened upon the item and brought it to Erzherzogin Isabella. With some trepidation she opened the fob, expecting to see a photograph or likeness of her daughter Maria Christina ... but instead found a likeness of her Hofdame, Sophie Chotek. After calming down somewhat, Isabella assumed it was merely a flirtation and that it would, of course, pass. Nevertheless, despite many years of faithful, flawless service, Gräfin Sophie Chotek was dismissed from the Erzherzogin's service immediately. The resulting outcry forced Franz Ferdinand to declare his love officially.

Sophie Maria Josephine Albina Chotek was the daughter of the Chief Equerry of the Imperial Court in Vienna, Bohuslaw Reichsgraf Chotek von Chotkowa und Wognin and of Gräfin Wilhelmine Kinsky von Wchinitz und Tettau – in 1898 Austro-Hungarian Consul in Dresden. The Choteks had been Bohemian barons since 1556, Gräfen of Bohemia since 1723, and from 1745 could also call themselves Reichsgraf. Two of the Choteks, Jan Rodolf (? – ?) and Karl (1783–1868) were even Ritter of the highly prestigious Austrian branch of the Order of the Golden Fleece. The Chotek escutcheon boasted sixteen quarterings of the most illustrious Bohemian ancestry, all of unimpeachable standing and of long and meritorious service to the Crown. But it was not enough.

By Habsburg Family Law there existed a small but august circle of families in standesgemäß – those deemed worthy of marriage to a Habsburg. A list published on 7th October, 1825, was headed by "fourteen princely houses domiciled in the Monarchy." To this were added the ruling houses of other European monarchies; for example the Wittelsbachs of Bayern and the Saxe-Coburgs of Sachsen were fecund courts for eligible spouses – the latter "the stud-farm of Europe," according to Bismarck. Also, Belgium and Portugal had recently supplied spouses to the late Kronprinz Rudolf and his uncle Erzherzog Karl Ludwig.

With both Elisabeth and Katharina Schratt no longer around, Emperor Franz Josef found some energy for a cause still left to him: the integrity of the House of Habsburg-Lothringen and his duty to it. Immediately he made it very clear to his nephew and Heir Apparent that he would not be allowed to marry Sophie Chotek, a "mere countess." The Emperor was backed to the hilt by every other Archduke and Archduchess of the Empire – including Franz Ferdinand's own brothers Otto and Ferdinand Karl, who asserted they were maintaining 'dynastic discipline' – as well as just about every other titled notable throughout the Dual Monarchy. Primus inter pares was Albert Fürst Montenuovo, Oberhofmeister, First Lord Chamberlain, of His Imperial Majesty, who repeatedly – and vehemently – reminded the Emperor of Sophie's lowly status. Montenuovo would remain Franz Ferdinand's arch-enemy throughout the remainder of the Thronfolger's life. And beyond.

By mid-summer 1899 it was entirely out in the open. Franz Ferdinand loved Sophie too much to give her up, and he persisted in his entreaties to the Emperor to approve their union. Franz Ferdinand demanded everything: his wife of choice, the Throne, and all rights that were due a Habsburg heir. Perhaps he knew this was impossible and that it would have to come down to bargaining. The press speculated about it. The coffeehouses buzzed with it. Franz Josef agonized over it. And both Franz Ferdinand and Montenuovo seethed because of it. Franz Ferdinand was not without sympathisers abroad: Kaiser Wilhelm II of Germany, Czar Nicholas II of Russia and Pope Leo XIII all made representations to Franz Josef on Franz Ferdinand's behalf, arguing that the row was undermining the stability of the Monarchy. But apart from a few of his immediate relatives – his stepmother and stepsisters – Franz Ferdinand found no allies in his own country. Enraged by the mounting enmity around him, Franz Ferdinand virtually shouted from the rooftops that he would marry Sophie Chotek ... or remain a bachelor forever. This was unthinkable for a Habsburg heir. Some sort of compact had to reached.

It was. Within a maelstrom of intrigue, courtiers, ministers, constitutional experts and jurist scribes debated and scratched away into the wee small hours to produce a humiliating solution. The insidious Montenuovo was behind it, of course. Franz Ferdinand had to perform a most humbling, not to say degrading, and almost public renunciation on behalf of his intended wife and future children. At noon on Thursday 28th June, 1900, in the council chamber in the Hofburg where a young Franz Josef had read out his own speech from the throne in 1848, and in the solemn presence of the Cardinal, the principal ministers of His Majesty's Government, all fifteen adult archdukes of the Habsburg family, the seventy-year old Emperor read out the terms of this "unique dynastic bargain:"

With gritted teeth and probably shaking with barely-controlled fury as the Prince-Archbishop of Salzburg held the Cross of Ferdinand above him, Franz Ferdinand signed the declaration of renunciation, together with its accompanying deeds in German and Hungarian, affixed his personal seal, all other Archdukes signed as witnesses, and within thirty minutes the council chamber was empty again. Three days later, Franz Ferdinand of Austria-Este married Sophie Chotek von Chotkowa und Wognin in the Sankt Franciscus Seraphicus chapel of Reichstadt (now Zákupy) castle in northern Bohemia. The local parish priest officiated the proceedings. The Emperor was not present. Nor was the Cardinal. Neither was any minister or, at the urging of Friedrich Herzog Teschen who had declared twelve days of mourning following the passing of a very minor member of the Habsburg family, any of the fifteen archdukes, including the groom's two brothers, his sister Margaretha Sophie, or any cousins – a personal insult he would not forget ...

The happy couple spent their honeymoon at Franz Ferdinand's estate at Schloß Konopischt with its magnificent gardens. Here he referred to their favourite walk as the Oberer Kreuzweg – the Upper Stations of the Cross, a bitter reminder of the degradations currently endured, as well as of those still to come. By way of a wedding gift – but probably as a means, however slight, not to add further injury to the House of Habsburg-Lothringen – Emperor Franz Josef created Gräfin Sophie Fürstin von Hohenberg (a minor Habsburg principality in southern Germany whose title had lapsed centuries earlier) with the qualification of Princely Grace [Diploma issued 8 August, 1900, back-dated to 1st July]; she could then be addressed as Most Serene Highness. This was both quite a mouthful and was still somewhat condescending. On 8th June, 1908, the Emperor granted the qualification of Serene Highness; Sophie could then be addressed as Serene Highness. On 4th October, 1909, she was created Herzogin von Hohenberg. While still not on a par with her archducal husband, the title did grant her the privilege of being addressed as Highness ad Personum, which was less socially awkward. Nevertheless, Franz Ferdinand and Sophie were extremely happy, as a letter to his stepmother Maria Theresia a week after the wedding demonstrates:

Although no 'classical' beauty, Sophie was a strikingly handsome and wholesome woman, with a serenity well suited to offset Franz Ferdinand's explosive temperament. Throughout their very happy marriage Sophie bore the most deeply wounding insults, snipes, snubs and humiliations with commendable dignity and fortitude. In private she may have cried into a handkerchief, but in public she held her head high and smiled openly – tut-tutting, calming and soothing her volatile, outraged husband who never let an opportunity pass to rail against the vicious indignities of protocol heaped on his beloved Sophie by the Court. For no degradation or insult was the Thronfolger's wife spared by Fürst Montenuovo and his cabal of Imperial courtiers. Throughout those fourteen years, at any Court or State function, Her Most Serene Highness Fürstin von Hohenberg – technically the 'Second Lady' of the Monarchy, or even the First, since Kaiserin Sissi had died – would have to enter alone, long after her husband; he would have to wait for Sophie to creep in at the tail end of protocol, after the youngest Archduchess had toddled-in in nappies. Sophie could never share a box with her husband at the opera or the theatre, never sit in the same Imperial carriage during state processions. In any official address Franz Ferdinand could never include the words, "My wife and I" ... Whenever Franz Ferdinand entertained a visiting sovereign at the Belvedere, she must remain invisible; Fürst Montenuovo had decreed that on such occasions the existence of a hostess could be acknowledged – but as a ghost: an extra place setting would be laid which would remain unoccupied. If Sophie stayed at the Belvedere after Franz Ferdinand had left, all sentries were promptly withdrawn as if nobody worth guarding were left behind. When Sophie organized a ball at Konopischt, Artstetten or Chlumetz, other Archduchesses and princelings organized bigger ones on the same date so that etiquette required guests to attend the latter. To the Habsburgs and the Court Sophie was a non-person. The renunciation of privileges also meant she would be denied the right of burial with her husband in the Habsburg family crypt, the Kapuzinergruft beneath the Kapuzinerkirche in Vienna. Franz Ferdinand's anger and resentment – indeed, any husband's anger and resentment at such wilful, malicious spite – must have been indescribable. In fact, it was perhaps small wonder that he visited Vienna as little as possible, often without Sophie, so as to spare her the vindictiveness of Fürst Montenuovo and the Vienna camarilla.

In public – and in the eyes and minds of the public, who felt he lacked charm and bonhomie – Franz Ferdinand had already been a quick-tempered, difficult-to-deal-with and abrasive man. His marriage did not soften or mellow him at all – at least not publicly. He was parsimonious, brusque, and did not suffer fools gladly. But he was what nowadays would be termed wysiwyg: what you see is what you get. He never attempted to improve his image or popularity – he never defended himself against criticism or refuted rumours spread about him by the news-hungry media (oh the times, they never a-change ...), but concentrated on the three passions of his life: his family, hunting and his military chancellery [see respectively The Family, The Proprietor and The Politician].