A large amount of dust from the Sahara reaches the Amazon Basin, as observed with satellite imagery. This dust is thought to carry micronutrients that could help fertilize the rainforest. However, considering different atmospheric transport conditions, different aridity levels in South America and Africa and active volcanism, it is not clear if the same pathways for dust have occurred throughout the Holocene. Here we present analyses of Sr-Nd isotopic ratios of a lacustrine sediment core from remote Lake Pata in the Amazon region that encompasses the past 7,500 years before present, and compare these ratios to dust signatures from a variety of sources. We find that dust reaching the western Amazon region during the study period had diverse origins, including the Andean region and northern and southern Africa. We suggest that the Sahara Desert was not the dominant source of dust throughout the vast Amazon basin over the past 7,500 years.