The production of yam-derived (Dioscorea rotundata) foodstuffs is mainly performed by small and medium scale processors that employ old traditional methods. This can lead to differences in quality from processor to processor, and from location to location, with consequent safety concerns. As such, the effects of processing and post-processing phases (i.e., storage, transport, etc.) on the safety of some yam-derived foodstuffs—namely chips, flakes, and flour—has been evaluated, with a focus on bacterial and fungal contamination, aflatoxins, pesticides, and heavy metals (Pb, Ni, Cd and Hg). Yams harvested and processed in Nigeria were screened, being that the country is the largest producer of the tuber, with 70–75% of the world production. Results highlighted no presence of pesticides, however, many samples showed high levels of bacterial and fungal contamination, together with heavy metal concentrations above the recommended safety levels. No trend was observed between the items considered; it was noticed, however, that samples purchased from the markets showed higher contamination levels than those freshly produced, especially regarding bacterial and aflatoxins presence. The processing stage was identified as the most critical, especially drying. Nonetheless, post-processing steps such as storage and handling at the point of sale also contributed for chemical contamination, such as aflatoxin and heavy metals. The results suggested that both the processing and post-processing phases have an impact on the safety of yam chips, flakes, and flour.