I know it's a bit late, but if interested, there's a lot of reading to be done for (some sections) of life under the rule of the Livonian Sword Brothers and Teutonic Order. These groups were operating in the Baltic territories from (roughly) the 13th century until the 16th century, and you can trace that back to earlier years in some cases, such as the border skirmishes going on between Poland and the Old Prussians.

There are a few things to note, and one of which is the degree of control that these holy orders actually had over an area. In many cases, especially involving the Teutonic Order, the earlier phases of pressing into territory involved actions that we might find similar to today's interactions between western military advisers and local Afghan or Iraqi populations. While the first wave of "settlers" into these pagan areas tended to be missionaries, the Pope wasn't too hesitant to grant military orders the right to protect the interests of these Christians, and these Order knights were often vastly out-manned and certainly out-gunned (one can find many examples, such as the Battle of Saule, among others) that demonstrate the effectiveness of the Prussians, Curonians, et cetera, operating in their native territory and utilizing hit-and-run tactics with their skirmishing groups. To establish any real foothold in the region, the knights worked with local nobility and collaborators to construct things such as garrisons, bridges, and roads, all with the intention of settling the area and fostering a sort of alliance with the locals. In many cases, these Order-friendly settlements were besieged by fellow pagans, who sometimes coerced the converts to return to paganism (as in Mazovia during the early 13th century). Again, without drawing too many parallels, you can imagine how the Taliban treated Afghan collaborators with Coalition forces. Many of these raiding groups didn't care about the ethnic makeup of the peasants - they were striking at the Christian infrastructure and Christian-aligned garrisons, as well as any pagan groups that opposed their interests. Peasants, which includes a rather wide sample of ranks and duties in these areas, were often the ones closest at hand during raids, since they generally lived outside of keep and garrison walls.

Aside from the obvious in-fighting going on here, there's a much darker side to the actions of groups like the Livonian Sword Brothers. The Papacy itself issued charges against them for doing things such as extorting money for conversions, taking slaves from the local population, executing ransomed hostages, and even abusing the local Christians (typically German by birth). We also need to remember that these are only the charges that they were formally accused of - there could be many more that were either ignored or unseen by Papal advisers, or were never uncovered, since the locals had little recourse in grievance matters. A 1249 document called the Treaty of Christburg outlines some of these issues in more detail, since it actively guaranteed rights to Christian converts among the Prussian clans. These rights prevented the Teutonic Order from abusing property sales and inheritance laws, and also forced the Prussians to submit tithes to local churches and aid in their construction. So, in essence, the peasants in these areas could be either German or locals (Prussians, Estonians, so on and so forth). The Germans settlers were Christian and typically received land as a result of settling there, and as such, they might be subject to raids or other dangers, but their customs, laws, and personal rights likely weren't violated to the same extent as the pagan Balts. There are some truly hideous stories about the fighting between the Balts and the Teutonic Order, but also stories about the Balts enslaving or massacring neighboring tribes during this period, all because of the in-fighting and the constant shifting of power between the collaborating and opposing tribes. Peasants, if defined as being non-fighting, non-noble locals of the area, had varying chances of prosperity and safety depending on their region. If you're interested in further reading, here are my sources, which delve much further into each region:

"The Northern Crusades" by Eric Christiansen. "The Prussian Crusade" by William Urban. "The Livonian Crusade" by William Urban. "Teutonic Knight: 1190-1561" by David Nicolle.

And, of course, the primary sources, which are the Treaty of Christburg, and the Livonian Sword Brother charges, found here: http://www.deremilitari.org/RESOURCES/SOURCES/baltic1.htm