Background: The major part of the edible oil used in Iran is supplied through imports. It is important to increase the yield of oilseed crops, especially soybeans, in non-chemical and environmentally friendly ways, along with its easy availability and low cost. The use of magnetic water as a new method, increases the yield of plants by improving solubility and access the nutrients. On the other hand, in recent years, methanol spraying as a source of carbon dioxide, which increases the concentration of this gas around the plant, enhancing the photosynthesis and plant yield. This study was conducted to study the efficacy of different intensities of magnetic water and various concentrations of methanol foliar application on agronomic traits of soybean. Methods: This experiment was carried out as split plot in a randomized complete block design with 3 replications during two consecutive years 2016-17. The main plot was irrigated with magnetic water in 4 intensity (0: control, 4, 8, 12mTesla) and a subplot was methanol spraying in 4 volumetric percentage (distilled water: control, 10, 20 and 30% v/v). Result: Photosynthetic pigments viz. (Chlorophyll a, b, carotenoid), yield attributes, seed yield, biological yield, seed protein and soybean economics were significantly affected by the magnetic water and methanol spraying. Seed yield and net return, as the most important traits increased by magnetic irrigated with 8 and 12mTesla intensities, compared to control, by 70.05-72.19% and 122.37-126.05%, respectively. Furthermore the maximum biological, stover yields and protein obtained by 8m Tesla magnetic irrigation, compared to control, it showed 59.54, 54.9 and 10.07% superiority, respectively. Also, methanol foliar application at 20% concentration increased seed yield, biological yield, seed protein and net return by 19.01, 13.73, 5.24 and 26.43%, respectively.