Reflecting Messerschmitt's belief in low-weight, low-drag, simple monoplanes, the armament was placed in the fuselage. This kept the wings very thin and light. Two synchronized machine guns were mounted in the cowling, firing over the top of the engine and through the propeller arc. An alternative arrangement was also designed, consisting of a single autocannon firing through a blast tube between the cylinder banks of the engine, known as a Motorkanone mount in German. This was also the choice of armament layout on some contemporary monoplane fighters, such as the French Dewoitine D.520, or the American Bell P-39 Airacobra, and dated back to World War I's small run of SPAD S.XII moteur-canon, 37 mm cannon-armed fighters in France.

When it was discovered in 1937 that the RAF was planning eight-gun batteries for its new Hawker Hurricane and Supermarine Spitfire fighters, it was decided that the Bf 109 should be more heavily armed. The problem was that the only place available to mount additional guns was in the wings. Only one spot was available in each wing, between the wheel well and slats, with room for only one gun, either a 7.92 mm MG 17 machine gun, or a 20 mm MG FF or MG FF/M cannon.

The first version of the 109 to have wing guns was the C-1, which had one MG 17 in each wing. To avoid redesigning the wing to accommodate large ammunition boxes and access hatches, an unusual ammunition feed was devised whereby a continuous belt holding 500 rounds was fed along chutes out to the wing tip, around a roller and then back along the wing, forward and beneath the gun breech, to the wing root, where it coursed around another roller and back to the weapon.

The gun barrel was placed in a long, large-diameter tube located between the spar and the leading edge. The tube channeled cooling air around the barrel and breech, exhausting out of a slot at the rear of the wing. The installation was so cramped that parts of the MG 17's breech mechanism extended into an opening created in the flap structure.

The much longer and heavier MG FF had to be mounted farther along the wing in an outer bay. A large hole was cut through the spar allowing the cannon to be fitted with the ammunition feed forward of the spar, while the breech block projected rearward through the spar. A 60-round ammunition drum was placed in a space closer to the wing root causing a bulge in the underside. A small hatch was incorporated in the bulge to allow access for changing the drum. The entire weapon could be removed for servicing by removing a leading edge panel.

From the 109F-series onwards, guns were no longer carried inside the wings. Instead, the Bf 109F had a 20 mm gun firing through the propeller shaft. The change was disliked by leading fighter pilots such as Adolf Galland and Walter Oesau, but others such as Werner Mölders considered the single nose-mounted gun to compensate well for the loss of the two wing guns. Galland had his Bf 109F-2 field-modified with a 20 mm MG FF/M autocannon, the "/M" suffix indicating the capability of firing thin-walled 20mm Minengeschoss shells, installed internally in each wing.

In place of internal wing armament, additional firepower was provided through a pair of 20 mm MG 151/20 cannons installed in conformal gun pods under the wings. The conformal gun pods, exclusive of ammunition, weighed 135 kg (298 lb); and 135 to 145 rounds were provided per gun. The total weight, including ammunition , was 215 kg. Installation of the under-wing gun pods was a simple task that could be quickly performed by the unit's armourers, and the gun pods imposed a reduction of speed of only 8 km/h (5 mph), By comparison, the installed weight of a similar armament of two 20 mm MG 151/20 cannon inside the wings of the Fw 190A-4/U8 was 130 kg (287 lb), without ammunition.

Although the additional armament increased the fighter's potency as a bomber destroyer, it had an adverse effect on the handling qualities, reducing its performance in fighter-versus-fighter combat and accentuating the tendency of the fighter to swing pendulum-fashion in flight.

Some of the projected 109K-series models, such as the K-6, were designed to carry 30 mm (1.18 in) MK 108 cannons in the wings.

Sources:
Gunston, Bill - The Encyclodepia of the Worlds Combat aircraft, 1976, Chartwell Books, Inc., New York
Brown, Eric, Captain - Wings of the Luftwaffe, 1979, Airlife Publishing Ltd., Shrewsbury
Gunston, Bill & Wood, Tony - Hitler's Luftwaffe, 1977, Salamander Books Ltd., London
Donald, David - The Complete Encyclopedia Of World Aircraft, 1997, Brown Packaging Books Ltd., London
Scutts, Jerry - Messerschmitt BF109: The Operational Record, 1996, Airlife Publishing Ltd, UK
Wikipedia - BF 109