Although the growth of graphene by chemical vapor deposition is a production technique that guarantees high crystallinity and superior electronic properties on large areas, it is still a challenge for manufacturers to efficiently scale up the production to the industrial scale. In this context, issues related to the purity and reproducibility of the graphene batches exist and need to be tackled. When graphene is grown in quartz furnaces, in particular, it is common to end up with samples contaminated by heterogeneous particles, which alter the growth mechanism and affect graphene’s properties. In this paper, we fully unveil the source of such contaminations and explain how they create during the growth process. We further propose a modification of the widely used quartz furnace configuration to fully suppress the sample contamination and obtain identical and clean graphene batches on large areas.