His order cited "credible evidence" that the proposed $140bn (£100bn) deal "threatens to impair the national security of the US".
Qualcomm is generally regarded as one of the leading companies in the development of 5G technologies and has invested huge amounts of money into its R&D in the field.
A major concern of a deal, which would have been the largest tech takeover deal in history, is that it would allow Huawei the chance to overtake both companies (currently sitting in the third spot for wireless technology). The order was issued based on ongoing security concerns the US has with Chinese telecoms firms doing business on home soil.
"Given the current political climate in the US and other regions around the world, everyone is taking a more conservative view on mergers and acquisitions and protecting their own domains," said Mario Morales, vice president of enabling technologies and semiconductors at global research firm IDC.
Others have labelled this latest move by Trump as merely about competition and ensuring the USA is first when it comes to the 5G arms race.