Biofortification has been used to improve micronutrient contents in crops for human consumption. In under-developed regions, it is important to fortify crops so that people can obtain essential micronutrients despite the limited variety in their diets. In wealthy societies, fortified crops are regarded as a “greener” choice for health supplements. Biofortification is also used in crops to boost the contents of other non-essential secondary metabolites which are considered beneficial to human health. Breeding of elite germplasms and metabolic engineering are common approaches to fortifying crops. However, the time required for breeding and the acceptance of genetically modified crops by the public have presented significant hurdles. As an alternative approach, microbe-mediated biofortification has not received the attention it deserves, despite having great potential. It has been reported that the inoculation of soil or crops with rhizospheric or endophytic microbes, respectively, can enhance the micronutrient contents in various plant tissues including roots, leaves and fruits. In this review, we highlight the applications of microbes as a sustainable and cost-effective alternative for biofortification by improving the mineral, vitamin, and beneficial secondary metabolite contents in crops through naturally occurring processes. In addition, the complex plant–microbe interactions involved in biofortification are also addressed.