The answer varies a lot depending on whether you mean the original, "Old Prussian" inhabitants of the Teutonic Order's territory, or the later settlers. The following is based on Preußen ohne Legende (1979) by Sebastian Haffner, which discusses the Teutonic Order as part of Prussia's "prehistory".

(EDIT: As others have pointed out, Haffner's description of the Order's crusade against the Old Prussians oversimplifies things. See the correction below.)

For the Old Prussians, the arrival of the Teutonic Order means pure, unmitigated suffering. They're a pagan people, viewed by their German and Polish neighbours as primitive savages, and the Order wages a brutal crusade against them. Anyone who refuses to be baptised is put to the sword. Haffner:

Heavily armed strangers burst into the land without provocation, demanded incomprehensible things in an incomprehensible language, and killed where they didn't find immediate obedience.

This goes on from 1226 to 1236. In 1260, the subjugated (and decimated) Old Prussians rise up against their conquerors; the Order's long campaign to suppress this revolt takes on a genocidal character. The Old Prussians are never exterminated entirely, but they're definitely on the brink.

On the ruins of the old Prussia, the Order establishes a new Prussian state with new Prussian people. They recruit settlers from various backgrounds: Germans, Poles, Kashubians, Masovians – as long as they're Christian.

The government of this new state is exceptionally modern for its day. Surrounded by feudal monarchies, the lands of the Order are instead ruled by a Grand Master, elected by the Order's knights, with a General Chapter acting as a council of ministers. Their territory is divided into provinces, each with a Komtur (governor) reporting to the central government. In a way, the religious knights of the Order act as paid civil servants.

Bound by monastic oaths of celibacy, the knights of the Order don't procreate; instead, they recruit new blood from Germany. Younger sons from German noble houses, eager for an alternative route to power and prestige, line up to join the Order. Haffner:

[The Order] can pick and choose the best candidates, and for a long time, it is governed very well.

And not only the Order itself attracts plenty of ambitious souls – their lands do, too. With plenty of fertile land whose original inhabitants have been violently wiped out, 14th-century Prussia is a "land of opportunity". (19th-century USA, anyone?) The new settlers work hard, and Prussia becomes the richest of the German colonies, with cities like Danzig and Königsberg growing quickly, and farmers enjoying much more wealth and liberty than in the surrounding feudal states.

Over time, however, the emerging New Prussian elite grow resentful of the Order. The Order maintains its policy of recruiting only from the Holy Roman Empire, meaning that Prussian locals – no matter how wealthy or prestigious – are excluded from political power in their own land. They jealously look over the border, to the growing power of the aristocracy in the kingdom of Poland. When Poland eventually annexes West Prussia and vassalises the east in 1466, many Prussians welcome the change from the Order's strict government to looser Polish feudal rule.

TL;DR: Crusades and genocide for the original inhabitants; prosperity and good governance – but no opportunities for a political career – for the later settlers.

EDIT/CORRECTION: /u/shlin28 and /u/Samskii requested that I elaborate on the point of the Order's crusade against the Old Prussians, and cite more sources; there was some concern that Haffner's description, quoted above, was a "sensationalised" version of the story. So, I've done some reading around. While obviously my search is constrained by what's available for free online, this is what I've found:

• The Teutonic Order came to Prussia at the request of Duke Conrad of Masovia. After repeated (peaceful and violent) attempts to christianise his Prussian neighbours, he called upon the Order for help in 1226. The Order was initially reluctant and it was not until 1230, when Conrad expanded his initial promises of land, that the knights of the Order actually arrived in Prussia.
• Their conquest of Prussia was a more complex and gradual process than described above. It focused on three elements: construction of castles, settlement by Christian immigrants, and subjugation-slash-enslavement of the Old Prussians.
• Officially, Christianisation "by the sword" (as Haffner describes) was not allowed; the knights of the Order were supposed to merely "pacify" the Prussians, and leave the missionary work to the Church. However, "pacification" is a term that can be interpreted widely. The knights repeatedly murdered Prussian men, took women and children prisoner, and burned down villages. The sources I've managed to find neither confirm nor deny that the "be baptised or die" tactic was ever actually used, though there are various unspecified references to "violent missionary campaigns".
• The Prussians revolted not once, but twice: once from 1242 to 1249, and once from 1260 to 1274. At the end of the first revolt, the Pope promised life and freedom to Prussians who agreed to be baptised within a month, but ordered the expulsion of any who refused. Many Prussians only let themselves be baptised for show, and continued to practise the old rites in secret.
• The Prussians recovered from their decimation by the Teutonic knights: by 1400, their population had recovered to more or less pre-conquest levels.
• As early as the first revolt, the Teutonic knights started to figure out internal Prussian politics, and tried to play different "factions" within the Prussian aristocracy against each other, rather than treating the Prussians as a single monolithic enemy.

To sum up: The Teutonic knights did commit plenty of atrocities against the Old Prussians. However, the situation was more complex than Haffner describes. The Order didn't always treat all Prussians as mortal enemies, but also as slaves, second-class citizens, or even allies of convenience in different times and places. Needless to say, I apologise for presenting a less-than-solid claim in an /r/AskHistorians answer, and I'll make sure to study a topic more thoroughly before posting in the future.

Sources:

• Jürgen Sarnowsky: Der Deutsche Orden – Entwicklung und Strukturen im Mittelalter (2000/2005)
• Jonathan Blümel: Die Kriegsführung des Deutschen Ordens im Baltikum (2012)
• Reinhard Wenskus: Der deutsche Orden und die nichtdeutsche Bevölkerung des Preußenlandes mit besonderer Berücksichtigung der Siedlung (1975)
• Klaus Wiegrefe: Gottesreich an der Ostsee (2007)

(Sorry, but English is not my native tongue)

As a second year Estonian history student, I've learned that Baltic-Germans built up a rigid class based system with ethnic borders. Locals were always the lowest of the low and towns (Tallinn/Reval, Tartu/Dorpat and Pärnu/Pernau) had always Baltic-German majority in them. During swedish rule (17th century) Swedish kings disliked how authoritarian local German nobility was. Teutonic order came to an end with Livonian war (end of 16th century), but Baltic-German nobles did not lose their positions.

Basicaly, till 19 century, local non-Germans had awful living conditions, being serfs till 1816/18, completely non-serfs in 1860s. Estonia was completely occupied by the crusaders in 1221. AfterJüriöö Uprising (~1345) serfdom really started kicking in and was escalating in 18th century, under the Russian rule. Jüriöö was very violently repelled, it was written in a chronicle that Harju county was empty of life. After the crusades some of the Estonian nobles had their high position in Northren danish part, there is not much information about Southern-Estonia, but it is known that North was more prosperous. It's also worth mentioning that in Danish part, nobles/manor owners were mostly Balti-German. After Jüriöö, none of the (supposed) Estonian noble families were left and Northren-Estonia was given to Teutonic Order. Local non-Germans were mostly peasants, very few were craftsmen or were holding any other position. With Lutherian reformation, some got positions to be pastors/priests. Fishing on the seas was banned, peasants had no right to move, all the land was owned by nobles and standards of living were horrible. One travel writing from 18th century mentions that peasants houses were small, full of smoke, had dirt floors and animals were living inside the house.

TL;DR Local non Baltic-Germans had it bad for very long, things got worse over time, till 19th century.

Source - Eesti Ajalugu/Estonian History by Seppo Settelberg