It has been suggested the breakdown of social order caused by the war was often more significant and longer lasting than the immediate damage. The collapse of local government created landless peasants, who banded together to protect themselves from the soldiers of both sides, and led to widespread rebellions in Upper Austria, Bavaria and Brandenburg. Soldiers devastated one area before moving on, leaving large tracts of land empty of people and changing the ecosystem. Food shortages were worsened by an explosion in the rodent population, while Bavaria was overrun by wolves in the winter of 1638, and its crops destroyed by packs of wild pigs the following spring.

The Peace of Westphalia reconfirmed "German liberties", ending Habsburg attempts to convert the Holy Roman Empire into a more centralised state similar to Spain. Over the next 50 years, Bavaria, Brandenburg-Prussia, Saxony and others increasingly pursued their own policies, while Sweden gained a permanent foothold in the Empire. Despite these setbacks, the Habsburg lands suffered less from the war than many others and became a far more coherent bloc with the absorption of Bohemia, and restoration of Catholicism throughout their territories.

France arguably gained more from the Thirty Years' War than any other power; by 1648, most of Richelieu's objectives had been achieved. These included separation of the Spanish and Austrian Habsburgs, expansion of the French frontier into the Empire, and an end to Spanish military supremacy in Northern Europe. Although the Franco-Spanish conflict continued until 1659, Westphalia allowed Louis XIV to begin replacing Spain as the predominant European power.

While differences over religion remained an issue throughout the 17th century, it was the last major war in Continental Europe in which it can be said to be a primary driver. It created the outlines of a Europe that persisted until 1815 and beyond; the nation-state of France, the beginnings of a unified Germany and separate Austro-Hungarian bloc, a diminished but still significant Spain, independent smaller states like Denmark, Sweden and Switzerland, along with a Low Countries split between the Dutch Republic and what became Belgium in 1830.