Information on the degradation of porous organosilicate glasses (OSGs) by active radicals and atoms is of high importance for their integration as low-k dielectrics in the next generation of ultra large scale integration (ULSI) production. The films’ degradation is caused by depletion of coverage of the pore surface methyl. OSG samples with differing porosities and pore sizes were treated by O, N, and F atoms at lowered temperatures (down to −45 °С) downstream of O2, N2, and SF6 inductively coupled plasma discharges, respectively. It has been shown that lowering the temperature reduces film degradation. In the case of O atoms, this reduction is insignificant, while the effect is much more noticeable for F atoms. In addition, an accumulation of F atoms forms a fluorocarbon layer during F atom treatment. The accumulated fluorine can interact with surface Si atoms, giving rise to film etching. The film degradation under O and F atoms increases with pore size and porosity, due to deeper atom penetration. In the case of N atoms, even a small temperature reduction essentially decreases OSG degradation, while –CH3 modification is less clear in the cases of O and F atoms. Density functional theory and ab initio molecular dynamics simulations of reaction mechanisms show that atom reactions with surface Si–CH3 groups are the initial stages of OSG degradation. Subsequent mechanisms include branched reaction pathways with the formation, modification, and destruction of different surface groups. In the cases of O and F atoms, these reactions lead to the formation of HxCО and CFx bonds. For the direct reaction of N(4S) atoms with –СН3 groups, significant activation energy is required. Under downstream plasma conditions, –СН3 groups are destroyed in reactions with metastable particles, and first of all, with metastable atoms N(2D), N(2P) and molecules , which are also produced inside the pores in the surface recombination of nitrogen atoms.