Bayer said in a statement that group net profit jumped 125.3 percent to 642 million euros ($899.3 million) in the period from July to September.
It noted, however, that profits in the same period a year earlier had been hit by a large provision for a lawsuit.
Overall group revenues grew by one percent to 8.67 billion euros in line with expectations and driven by markets in Asia, Latin America, Africa, the Middle East and Eastern Europe, Bayer said.
Business in the Western European and North American markets did not fair so well, notably as a result of health care reforms which hit medicine sales in the US in particular.
Bayer said its agrochemicals division, CropScience, which produces fertilizer among other things, had benefited from higher prices of agricultural raw materials.
However, raw material and energy costs had dragged down profits in its chemicals division, Bayer said.
Unlike its rival BASF, which also published its third-quarter results Thursday, Bayer said it did not see a slowdown in demand.