The hydrogen is catalytically reacted with nitrogen (derived from process air) to form anhydrous liquid ammonia. It is difficult and expensive, as lower temperatures result in slower reaction kinetics (hence a slower reaction rate) and high pressure requires high-strength pressure vessels that resist hydrogen embrittlement. Diatomic nitrogen is bound together by a triple bond, which makes it relatively inert. Yield and efficiency are low, meaning that the ammonia must be extracted and the gases reprocessed for the reaction to proceed at an acceptable pace.
This step is known as the ammonia synthesis loop:
The gases (nitrogen and hydrogen) are passed over four beds of catalyst, with cooling between each pass to maintain a reasonable equilibrium constant. On each pass, only about 15% conversion occurs, but unreacted gases are recycled, and eventually conversion of 97% is achieved.
Due to the nature of the (typically multi-promoted magnetite) catalyst used in the ammonia synthesis reaction, only low levels of oxygen-containing (especially CO, CO and HO) compounds can be tolerated in the hydrogen/nitrogen mixture. Relatively pure nitrogen can be obtained by air separation, but additional oxygen removal may be required.
Because of relatively low single pass conversion rates (typically less than 20%), a large recycle stream is required. This can lead to the accumulation of inerts in the gas.
Nitrogen gas (N) is unreactive because the atoms are held together by triple bonds. The Haber process relies on catalysts that accelerate the scission of these bonds.
Two opposing considerations are relevant: the equilibrium position and the reaction rate. At room temperature, the equilibrium is in favor of ammonia, but the reaction does not proceed at a detectable rate due to its high activation energy. Because the reaction is exothermic, the equilibrium constant decreases with increasing temperature following Le Châtelier's principle. It becomes unity at around .
Above this temperature, the equilibrium quickly becomes unfavorable at atmospheric pressure, according to the Van 't Hoff equation. Lowering the temperature is unhelpful because the catalyst requires a temperature of at least 400 °C to be efficient.
Increased pressure favors the forward reaction because 4 moles of reactant produce 2 moles of product, and the pressure used () alters the equilibrium concentrations to give a substantial ammonia yield. The reason for this is evident in the equilibrium relationship:
where  is the fugacity coefficient of species ,  is the mole fraction of the same species,  is the reactor pressure, and  is standard pressure, typically .
Economically, reactor pressurization is expensive: pipes, valves, and reaction vessels need to be strong enough, and safety considerations affect operating at 20 MPa. Compressors take considerable energy, as work must be done on the (compressible) gas. Thus, the compromise used gives a single-pass yield of around 15%.
While removing the ammonia from the system increases the reaction yield, this step is not used in practice, since the temperature is too high; instead it is removed from the gases leaving the reaction vessel. The hot gases are cooled under high pressure, allowing the ammonia to condense and be removed as a liquid. Unreacted hydrogen and nitrogen gases are returned to the reaction vessel for another round. While most ammonia is removed (typically down to 2–5 mol.%), some ammonia remains in the recycle stream. In academic literature, a more complete separation of ammonia has been proposed by absorption in metal halides or zeolites. Such a process is called an absorbent-enhanced Haber process or adsorbent-enhanced Haber–Bosch process.