Nowadays, the raising in agriculture productions is required to meet the demand for growing population. Besides macronutrients (nitrogen, phosphorus and potassium, and to a lesser degree, calcium, sulfur and magnesium) requirements, plants need micronutrients (copper, iron, zinc, boron...) to ensure productivity as well as high agricultural quality. The activity of these elements is greatly affected by very small changes in environmental factors such as pH, mechanical composition and organic matter in the soil. Therefore, there must be another way to effectively bring these elements to the crop. This leads to research and development of a new fertilizer to provide nutrients more effectively. This study reports the synthesis of a new nanofertilizer incorporating micronutrients with hydroxyapatite (nHA) and its impacts on Asparagus officinalis germination. FESEM images show that the nanofertilizer particles were in rod-shaped with diameters of 20–25 nm and length of approximately 86 nm, while EDX image reveals micronutrient compositions: Ag (696 mg kg−1), Zn (619 mg kg−1), Cu (427 mg kg−1), Co (519 mg kg−1g) and Fe (751 mg kg−1). The 10-day-long Asparagus officinalis seeds test proved a faster germination rate (46.4 ± 1.2 mm/10 days) compared to that of normal treatment (35.3 ± 0.8 mm/10 days). When asparagus was used the micronutrients nano system, they had the ability to grow faster than unused. These results suggest promising application of nanoferitilizer in agriculture.