This version of Godzilla is somewhat passive and seemingly unaware of humanity at first, only causing destruction due to the cumbersome and clumsy nature of his earlier forms, then later as a result of his final form's size as he walks through Tokyo. Godzilla does not retaliate against the JSDF when they attack him and seems to barely notice their assault. However, when American B-2 Stealth Bombers drop bunker-buster bombs onto his back and actually injure him, Godzilla becomes enraged and immediately retaliates with his atomic breath, not only destroying the attacking forces but obliterating a huge part of Tokyo at the same time. When Godzilla is assaulted at the film's climax, he retaliates against the humans using his atomic breath and various beam attacks.

His form much more resemblance to past Godzilla designs than the previous forms, though it does bear some differences. The fourth form is reminiscent of the original 1954 Godzilla design, with a rounded head with small beady eyes and black, scarred and bumpy skin. This form's dorsal plates are black in color and much larger than the previous form, and also possess red scales on them reminiscent of keloid scars. Godzilla's mouth lacks a tongue and is full of crooked and incredibly large teeth, some of which are growing from the flesh outside of his mouth. When Godzilla fires his atomic breath, his upper jaw unhinges from his lower jaw, which splits open. The eyes are small compared to the previous forms, and appear sunken into their sockets, with no eyelids surrounding them. In place of eyelids, this form has silvery nictitating membranes, called anti-flash defensive membranes, that cover its eyes and protect them from harm. The arms are more developed than in previous forms, but are still very small and do not extend far beyond Godzilla's chest, which bears a prominent, axe-shaped pointed sternum. The legs are larger and more muscular, while Godzilla's feet bear numerous small vestigial toe claws growing from their tops and sides in addition to five main digits. Godzilla's flesh is covered in reddish scars and lesions that sometimes emit a reddish glow, which changes to purple when Godzilla charges his atomic breath. Godzilla's tail is very long, and has small spike-like dorsal plates running along its length. The tip of Godzilla's tail is red and bloody and covered in twisted mangled bones, which form a skeletal spare head (予備頭部 Yobi tobu) at the end

Shin Godzilla retains the character's trademark atomic breath. This Godzilla's signature weapon initially takes the form of a cloud of smoke exhaled from his mouth and then a stream of fire, called the Super Thermal Radiation Particle Belt Flame (超高熱放射性粒子帯焔 Chō Kōnetsu Hōshasei Ryūshi-taien) or Thermal Flame (熱焔 Netsuen) for short, which is capable of burning through entire city blocks at high speed. From there, he focuses the fire into a narrow, purple stream of atomic breath (放射熱線 Hōsha Nessen, lit. "Radiation Heat Beam"), which slices through buildings and strikes distant targets. When firing the atomic breath, Godzilla's body emits a purple glow, which is concentrated around his dorsal fins. Godzilla's upper jaw then unhinges from his lower jaw, which splits apart to make room for the beam to be fired. After expending a lot of energy, Godzilla's beam weakened back to a stream of fire before petering out.

One of Godzilla's most unique abilities is his capacity to self-mutate. While all other organisms mutate and evolve gradually over countless generations, Godzilla has the ability to mutate his DNA at will to adapt to any situation. According to characters in the film, Godzilla is the most evolved creature on the planet, possessing eight times the genetic information of human beings. Godzilla started out as a type of prehistoric sea creature that adapted to feed on nuclear waste in its habitat, then continued growing and evolving over a period of 60 years. After destroying the Tokyo Bay Aqua-Line, Godzilla evolved into his second form, developing legs capable of bringing him on land. After wandering through Tokyo, Godzilla evolved further into his third form, developing longer arms and standing upright on two legs. When he surfaced once more at Kamakura, Godzilla had reached his fourth form, which was almost twice as large as his third form and possessed heavily armored skin which made him immune to conventional human weaponry. After being injured by B-2 Bombers, Godzilla adapted to use the atomic energy he generated as a weapon, firing it from his mouth and dorsal fins in the form of purple lasers that could slice through any object. While hibernating in Tokyo, the mouth on the end of Godzilla's tail split open, giving him the ability to now fire his atomic beam from the tip of his tail. After Godzilla was frozen by blood coagulant, small humanoid creatures with Godzilla's teeth and dorsal plates, Godzilla's fifth form, could be seen fissioning from Godzilla's tail, suggesting that he was in the process of evolving into an army of human-like forms capable of combating humanity.

Like all versions of Godzilla, Shin Godzilla is extremely durable and resistant to most conventional weaponry. When assaulted by the JSDF's AH-64 Apache and AH-1 Cobra helicopters and Type 10 Tanks, Godzilla did not seem at all aware of their attacks and was completely unharmed. Even bombs dropped directly onto Godzilla by fighter jets were unable to harm him, though he did respond to their attacks by deploying protective membranes over his eyes. The only military weapon capable of harming Godzilla was the Massive Ordnance Penetrator (MOP II) bomb used against him by American B-2 bombers. Though this bomb did draw blood from Godzilla and sever one of his dorsal fins, he quickly recovered. In addition, the dorsal plate that was severed was later found by a reconnaissance team in the process of regenerating on its own. The characters speculated that it was possible for individual pieces of Godzilla to regenerate into functioning creatures, allowing Godzilla to rapidly spread all over the world.

Shin Godzilla's atomic energy can also be redirected and fired from the tip of his tail. This beam is apparently fired from a mouth on the vestigial "spare head" at the end of Godzilla's tail. Unlike the dorsal plate beams, the tail beam can be fired at the same time as Godzilla's atomic breath, allowing him to strike multiple targets at once.

Shin Godzilla can also redirect his atomic energy to fire numerous purple beams from in between his dorsal fins. These beams are capable of destroying objects thousands of meters around Godzilla and are comparable to his atomic breath in power.