Sub microscopic refractory gold ore is an important resource of gold with the depletion of free-milling gold deposits in this century. It has been generally accepted that submicroscopic gold mainly in the form of solid-solution and colloidal particles are physically locked inside mineral phases and impervious to cyanide solution. However, some researches on synthetic nanoparticles show they have very different physical and chemical properties which can affect their dissolution behavior.This research has been conducted to investigate the dissolution behavior of gold sub microscopic particles experimentally and theoretically using density functional theory. For this purpose, 20 nm gold particles have been synthesized and dissolved in cyanide solution under controlled condition. The rate of dissolution has been monitored during cyanidation and compared with a gold disk. The results depict the rate of dissolution per surface area is significantly reduced in gold nanoparticles (30 times, the surface ratio of 14/9 m2/g and 0.006 m2/g in samples is 2500 times smaller while the dissolution rate in nanoparticles is 83 times faster). Also, the smaller nanoparticles have much slower dissolution kinetics than large nanoparticles (5.485 × 10−5 and 4.280 × 10−6 g/m2.s for 16 and 2 nm particles, respectively). Two different dissolution regimes can be identified for >3 nm and < 3 nm nanoparticles. In larger particles, by increasing the number of surface atoms with weaker bond energy and also lower oxidation potential, the dissolution rate increases compared to bulk gold. In nanoparticles smaller than 3 nm, the electrochemical reaction in the cyanide medium is disrupted by the reduction of oxidation potential and decreasing the conductivity as the requirement for electrochemical dissolution of gold in cyanide.The molecular modeling study on the gold clusters of 1 to 20 atom confirm that the oxidation of small clusters of gold is more difficult than bulk gold due to the high ionization energy (9.66 vs. 5.4 eV). Also, the monoatomic gold has a much weaker interaction with cyanide (−4.36 vs. -1.6 eV) and higher interaction with oxygen (−0.64 vs. -0.15 eV) compared to the bulk gold. The HOMO of monoatomic and bulk gold (−9.22 and − 4.5 eV) as well as LUMO of cyanide and oxygen (1.734 and − 4.657 eV), as two reactants in cyanidation process confirm the results based on HSAB theory. As a result, oxygen competes with cyanide for adsorption on the surface of gold nanoparticles, disrupting the first step of electrochemical dissolution of gold, as the adsorption of cyanide and the formation of the Au-CN− complex. This is possible by deactivating the surface by creating a resistant layer of gold oxide or electrostatic adsorption of oxygen on the gold surface and passivating the surface. The modeling data are very well in agreement with the experimental results indicating the inherent inactivity of free surface gold sub microscopic particles during the cyanidation process.