Agriculture waste has attracted attention as a potential source to produce raw material silicon dioxide, either crystalline (pyrophyllite) or amorphous form (geothermal sludge). It is an unwanted waste produced as a desired result of agricultural activities. Nanosilicon dioxide has undoubtedly gained eager interest in many vital industries. It is renowned for positively enhancing outstanding performance due to tuneable properties over its bulk counterpart. Silicon dioxide scientifically demonstrates a unique ability to convert efficiently into economic value from silicon-rich agriculture waste. Thus, a noble extraction from silicon-rich waste is undoubtedly gaining enormous attention. However, adequate knowledge on local optimisation of nanosilicon dioxide extraction from silicon-rich agriculture waste is lacking. Specific aims of this comprehensive review mainly highlighted a synthesis method of potential nanostructured silicon dioxide from agriculture waste and their potential applications for plant growth promoters. Reverse microemulsion, chemical vapour condensation, solid gelation, and mechanochemical are preferred methods that were typically specified to focus this comprehensive review critically. Optimisation of nanosilicon dioxide can be achieved precisely via the ideal combination of solid gelation and a high-energy ball mill process. Silicon dioxide is undoubtedly an effective agent as a plant growth promoter to overcome biotic and abiotic factors such as heavy metal uptake and translocation, inhibit pathogenic fungi, improve the antioxidant system, and mitigate various stress factors.