Cells can form ATP in more than one way. Substrate-level phosphorylation makes ATP by transferring a phosphate group directly from a phosphorylated reaction intermediate to ADP.

The generic pattern is

$$\mathrm{X{-}P+ADP\rightarrow X+ATP},$$

where $\mathrm{X{-}P}$ is a sufficiently reactive phosphorylated substrate.

The ATP-producing reaction is favorable because it is coupled to conversion of the phosphorylated intermediate into a lower-free-energy product.

Direct chemical transfer defines the mechanism

In substrate-level phosphorylation, ADP receives phosphate through an enzyme-catalyzed chemical reaction involving the substrate itself. No membrane ion gradient is needed for the ATP-forming step.

This is mechanistically different from membrane-based ATP formation, where an electrochemical gradient drives a molecular ATP-making machine. Both routes ultimately produce the same ATP molecule, but they capture free energy in different ways.

Worked bookkeeping example

Suppose one pathway molecule is converted into two equivalent intermediates, and each intermediate later performs two ATP-forming substrate-level phosphorylation reactions.

That produces

$$2\times2=4\ \mathrm{ATP}.$$

If preparing the intermediates earlier required consumption of two ATP, the pathway's net ATP contribution is

$$4-2=2\ \mathrm{ATP}.$$

This is the bookkeeping pattern used in glycolysis: ATP can be invested in early coupled reactions and regenerated later by direct phosphate transfer.

Substrate-level phosphorylation does not require oxygen directly

Because the immediate ATP-forming step is a local chemical group-transfer reaction, it does not consume molecular oxygen. Whether the surrounding pathway can continue may still depend on recycling other reactants such as oxidized electron carriers.

Substrate-level phosphorylation is therefore best defined by how ATP is made, not by whether the organism or pathway is aerobic or anaerobic.