Developing sustainable technology to grow nutritious produce under controlled environment is an important strategy to practice urban agriculture. Being rich in nutrients and having a short growth cycle, sprouts and microgreens are regarded as microscale vegetables that become ideal candidates for indoor farming. But as immature plants, sprouts and microgreens are highly perishable fresh produce, particularly vulnerable to microbial contamination, long-distance transportation, and storage. Various cultivation substrates, including fiber-based soil substitutes, hydroponics, and aeroponics, are being studied as alternatives to traditional soil for growing such specialty crops. The advantages and disadvantages of each cultivation method are critically reviewed. Hydrogel-based soilless cultivation as a new and innovative practice is especially highlighted for its uniqueness to tackle food safety and sustainability challenges to grow sprouts and microgreens toward urban agriculture.