They were certainly brutal if you believe the sources from that time. Kurt Villads Jensen states that the impression one gets from many of these chronicles is “one of mass killing or - if practically possible - enslavement of the enemies.” I’ll relate some incidents described in the chronicles dating from that period.

Heinrich von Hervord whose chornoicle ends in the year 1355 gives us a glimpse of the zeal of the Teutonic Knights, writing “The kingdom of the Poles [this then included Prussia] was destroyed and desolated. They slew the king in his own kingdom, in his own house; nay, they seized him in bed. They wasted and ravaged and ruined the whole kingdom with fire and sword. Cities, towns, castles, estates, seized and held for themselves as a possession forever by right of war"; and further on "They think they hold Prussia by full right, though the original possessors [Prussians] never to this day cease from their earnest desire to recover it."

Other chronicles go into more detail about the atrocities. They are rarely (if ever) disapproving about these atrocities or express any sympathy, but they seem to almost glory in it at times.

The Thuringian Chronicon Sampetrinum relates: “The enemies of the Cross of Christ raided Prussia with four companies of cavalry. They killed thirteen brothers of the Teutonic House. They carried away with them Christian captives and spoil. They burned some country-houses and many of their occupants."

The vengeance was swift and terrible. And In the Annals of Prague (1196-1278) we read: “The Prince of Bohemia and the Margrave of Brandenburg entering Prussia laid it waste and despoiled it with fire and plunder. They slew many with every form of death, sparing neither sex or age.” The two items are equally commonplace to the chronicler, and the sparing of neither age nor sex is a recurring motif throughout all the chronicles. The retaliation must have been quite brutal as it brought results. The Annals of Ottokar (1254-78), in treating of this same year (1255), tell us: "Meanwhile the leaders of Prussia, moved, as we believe, by the fear of God and by the very sound of the name of the Prince of Bohemia, came in all humility to this Prince."

One of the most brutal incidents related in the chronicles is when the Knights seized Pippin of Pomerania’s swamp castle. Pippin was betrayed into the hands of the Teutonic Knights by his own brother-in-law: "He, that he might escape death, led the Brothers thither with an army while the garrison lay drunken after a revel. Bursting violently in, they killed or captured all and reduced the castle to ashes." Pippin himself "the Brothers dragged away tied to the tail of a horse and hanged him to a tree" (The chronicle of Prussia, book III). The Ancient Chronicle of Oliva gives a still more horrible account of the death of the unfortunate Pippin: "His abdomen they opened at the navel. They fastened the navel to a tree and compelled him by force to run around the tree until he was totally disembowelled.”

On one occasion a chronicle tells us that the knights captured an aged noble who they converted to Christianity. After this, they released him and gave him a banner that should now protect him in case of a raid. He left for home but for him "he was a little too slow, not knowing how impetuous the Teutons were in war." And when he reached his lands "he found his own and his people's houses burned, the members of his own and his people's households and his brother and his kin slain” (Chronicle of Prussia, book III). The same chronicle also tells the story of the Teutonic knight named Volrad the wonderful who invited many Prussian nobles to a feast in his castle and “When they were intoxicated and began to mutter threats he slipped out, barring the doors, he reduced to ashes both the nobles and the castle.”

Another incident of incineration is recorded: “The same time the brothers from Ragnit took their people to Gediminas’s castle in Lithuania, travelling secretly at night. At dawn, when everyone was still asleep they attacked and set fire to the outer bailey. Everything in it was burned: men, women, possessions and livestock were all completely incinerated…only 12 Lithuanians escaped from the castle and were not burned to death.” (Chronicle of Prussia, book III).

Although you must note that German Knights weren’t always the ones committing the atrocities nor was their cruelty anything unusual for that time. The Knights were able to quite successfully recruit native Balts as auxiliaries in large numbers, who tended to be equally brutal according to the chronicles

“What made them more formidable was their ability to enlist the support of indigenous peoples, and for this intimidation was not sufficient. Nor was persuasion by the word: Henry of Livonia makes it clear that there were never more than a few who were prepared to renounce the old gods and fight for the new without other inducements…The adherence [also] came about because of material inducements, such as the aid the crusaders were prepared to give to Livs and Letts in raiding the Estonians – a chance to settle old scores and get rich.” - The Northern Crusades, Eric Christiansen

For instance, German knights from Riga had allied with the pagan Semigallians, living south of Riga, whom they gave the Lithuanian and Estonian prisoners to guard. The Semigallians soon killed most of the Estonian prisoners with the sword, because “they were old enemies” (Henry of Livonia, 1227). The Christians did not reproach the Semigallians for this killing, however, because there were still plenty of prisoners and of booty to be divided among the warriors.

Otherwise, the chronicles are often quite repetitive when it comes to the atrocities and the expeditions carried out. As Kurt Villads Jensen states, “This was the typical pattern, repeating itself, expedition after expedition, year after year. Men killed in the first attack, women and children taken captives, but when the crusaders returned a second time and when military control had been secured, also men were taken prisoners. This way of conducting war seems to have been common both to Christians and to pagans.”