In 1186, the younger Baldwin married Marie of Champagne, daughter of count Henry I of Champagne. The chronicler Gislebert describes Baldwin as being infatuated with his young bride, who nevertheless preferred prayer to the marital bed. Gislebert claims Baldwin was "tied only to one woman", his wife. Through Marie, Baldwin had additional connections and obligations to the defenders of the Holy Land: Her brother Henry II of Champagne had been King of Jerusalem in the 1190s (leaving a widow and two daughters who needed help to keep and regain their territories in Palestine). Marie's uncles Richard I of England and Philip II of France had just been on the Third Crusade.
Baldwin's own family had also been involved in the defence of Jerusalem: his uncle Philip had died on Crusade. Baldwin's mother's mother was great-aunt of Isabella, Queen of Jerusalem and the Counts of Flanders had tried to help Jerusalem relatives in their struggle. Baldwin wanted to continue the tradition. Margaret died in 1194, and the younger Baldwin became Count of Flanders. His father died the next year, and he succeeded to Hainaut.
In this fight against the French king, Baldwin allied with others who had quarrels with Philip, including kings Richard I and John of England, and the German King Otto IV. A month after the treaty, on February 23, 1200, Baldwin took the cross -- that is, he committed to embark on a crusade. He spent the next two years preparing, finally leaving on April 14, 1202.
As part of his effort to leave his domains in good order, Baldwin issued two notable charters for Hainaut. One detailed an extensive criminal code, and appears to be based on a now-lost charter of his father. The other laid down specific rules for inheritance. These are an important part of the legal tradition in Belgium.
Baldwin left behind his two-year-old daughter and his pregnant wife, Countess Marie. By early 1204, she had left both her children behind to join him in the East. They expected to return in a couple of years, but in the end neither would see their children or their homeland again. Marie was regent for Baldwin for the two years she remained in Flanders and Hainaut. Afterward, Baldwin's younger brother Philip of Namur was regent and also had custody of the daughters. Baldwin's uncle William of Thy (an illegitimate son of Baldwin IV of Hainaut) was regent for Hainaut.
Meanwhile, the crusade had been diverted to Constantinople, where the crusaders had captured and sacked the city, and decided to set up a Latin empire in place of the fallen Greek one.
The Latin Empire was organized on feudal principles; the emperor was feudal superior of the princes who received portions of the conquered territory. His own special portion consisted of the city of Constantinople, the adjacent regions both on the European and the Asiatic side, along with some outlying districts, and several islands including Lemnos, Lesbos, Chios and Tenos. The territories still had to be conquered; and first of all it was necessary to break the resistance of the Greeks in Thrace and secure Thessalonica. In this enterprise in the summer of 1204, Baldwin came into collision with Boniface of Montferrat, the rival candidate for the empire, who was to receive a large territory in Macedonia with the title of King of Thessalonica.
Boniface hoped to make himself quite independent of the empire, to do no homage for his kingdom, and he opposed Baldwin's proposal to march to Thessalonica. The antagonism between Flemings and Lombards aggravated the quarrel. Baldwin insisted on going to Thessalonica; Boniface laid siege to Adrianople, where Baldwin had established a governor; civil war seemed inevitable. An agreement was effected by the efforts of Dandolo and the count of Blois. Boniface received Thessalonica as a fief from the emperor, and was appointed commander of the forces which were to march to the conquest of Greece.
During the following winter (1204–1205) the Franks prosecuted conquests in Bithynia, in which Henry, Baldwin's brother, took part. But in February the Greeks revolted in Thrace, relying on the assistance of John (Kaloyan), tsar of Bulgaria, whose overtures of alliance had been rejected by the emperor. The garrison of Adrianople was expelled. Baldwin along with Dandolo, the count of Blois, and Marshal Villehardouin, the historian, marched to besiege that city. The Frankish knights were defeated (April 14, 1205); the count of Blois was slain, and the emperor captured by the Bulgarians (see Battle of Adrianople).
For some time his fate was uncertain, and in the meanwhile Henry, his brother, assumed the regency. Not till the middle of July was it definitely ascertained that he was dead. The circumstances of Baldwin's death are not exactly known. It seems that he was at first treated well as a valuable hostage, but was sacrificed by the Bulgarian monarch in a sudden outburst of rage, perhaps in consequence of the revolt of Philippopolis, which passed into the hands of the Franks. According to a Bulgarian legend, Baldwin had caused his own downfall by trying to seduce Kaloyan's wife. The historian George Acropolites reports that the Tsar had Baldwin's skull made into a drinking cup, just as had happened to Nicephorus I almost four hundred years before. At any rate, Tsar Kaloyan wrote to Pope Innocent III, reporting that Baldwin had died in prison. A tower of the Tsarevets fortress of the medieval Bulgarian capital, Veliko Tarnovo, is still called "Baldwin's Tower".
It was not until July 1206 that the Latins in Constantinople had reliable information that Baldwin was dead. His brother Henry was crowned emperor in August.
Back in Flanders, however, there seemed to be doubt whether Baldwin was truly dead. In any case, Baldwin's other brother Philip of Namur remained as regent, and eventually both of Baldwin's daughters Jeanne and Margaret were to rule as countesses of Flanders.
Twenty years later, in 1225, a man appeared in Flanders claiming to be the presumed dead Baldwin. His claim soon became entangled in a series of rebellions and revolts in Flanders against the rule of Baldwin's daughter Jeanne. A number of people who had known Baldwin before the crusade met the supposed count and emperor and rejected his claim. In the end he was executed in 1226.