Soul Menace (魂威, Kon'i): Franken Stein is a powerful practitioner of the special art known as Soul Menace, in which allows him to apply his own Soul Wavelength offensively without the usage of a weapon. This ability allows him to attack with a variety of techniques in which mimic the properties of electricity. This move also allows him to deal deadly internal damage powerful enough to negate the usage of the Black Blood from Crona/Ragnarok after three usages during their battle as well as send his opponents at a distance due to it's powerful force as well has a variety of technique variation thanks to this art as well as easily "kill" White Rabbit in one hit. Black☆Star once remarked that unlike himself, Stein is able to fire Soul Menaces consecutively without build-up.
- Consecutive Soul Menace Three-Fold! "Gi" "Go" "Shoku" (掌魂威 参極「魏」「呉」「蜀」, Renshō Kon'i - Sangoku "Gi" "Go" "Shoku): A variation of the Soul Menace technique, that instead rapidly hits an opponent three times in succession, using the same fist. The attack inflicts enough internal damage to cause the target to bleed from the mouth.
- Two Palm Soul Menace - Twin Spears (二掌魂威・双槍, Nishō Kon'i - Sōsō ):A variation of the attack Soul Menace that instead makes use of both hands, rather than just one. However, due to the inclusion of an extra hand, the attack's power is greatly amplified and able to incapacitate even strong opponents.
Soul Perception (魂感知, Tamashī Kanchi): Franken Stein is able to sense and perceive the souls of other beings. Unlike most Meisters, not only can he simply see the souls himself, but is also so high-rate that he can read an individual's personality, characteristics and Soul Wavelength.
Utility Meister (ユーティリティ職人, Yūtiriti Shokunin): As a powerful Meister and capable fighter, Stein has learned how to wield all different kind of weapons.
- Scythe-Meister (鎌職人, Kama Shokunin): Mainly, Franken Stein is known to be an extremely skilled Scythe-Meister and normally employs Death Scythe as his main weapon of choice when using a scythe. As a Scythe-Meister, he's very adept at handling a Scythe enough to spin and twirl a scythe weapon with ease. When using Spirit, his fighting style revolves around the using his scythe weapon as a shield to block attacks and immediately counter-attack with his left hand with powerful attacks such as Soul Menace. His skill has enabled him to outmatch Crona using the Demon Sword against him He also was able to hold his own with the witch, Medusa, and eventually won.
- Lamp Meister (ランプ職人, Ranpu Shokunin): Stein has shown the ability to use a Lantern as a weapon such as the Demon Lamp. While able to use it similar Kim Diehl's method, he can also improvise and use it like that of a propeller for his fists for extra damage, having done so against Soul Evans when he found he couldn't allow the formidable Death Scythe to touch the normal Demon Weapon without Jacqueline feeling pain due to the difference in power between the two weapons.
- Hammer Meister: In addition to being skilled with a Scythe, Stein also is seen mainly using Mjolnir, capable of using in both the hammer form and the tonfo form, being able to easly take on Justin Law where he would even resort to retreating when Stein used Mjolnir's Lightning Rope, even when the rogue Death Scythe merged with the Clown and used his abilities as a stationary weapon to his advantage, Stein manage to defeat and kill Justin.
Master Hand-to-Hand Combatant: Stein seems to be a master of hand-to-hand combat, having been seen occasionally training by himself. With his unarmed combat skills combined with his various skills, he's been able to take down Maka Albarn and Black☆Star with they both used their weapons in their first altercation and seemingly gotten the upper-hand in his spar with Black☆Star. He's also not above with abandoning the use of his weapon and relying on some of his unarmed ability, evident as he did so during his battle against Crona.
Enhanced Strength: Stein has enough strength to kick Crona away a fair distance away when he saved Maka as well as break down the Santa Mario Novella Basilica with a kick whearas Maka wasn't able to push open due to the doors only opening inwards. His punch also managed to send Black☆Star a distance away.
Enhanced Speed: Stein possesses incredible speed, moving fast enough to appear as a blur as he rushed to Medusa during his fight with her. He also managed to allude Ragnarok's eye sight moments after performing Experimental Ectoplasm and when the weapon quickly emerged from Crona's body.
Enhanced Durability:Stein has taken multiple bloody-needles from Crona on his side of both his body and head and continued to be able to fight despite the injuries. He's also survived being drilled though and hit by Medusa Gorgon's Vector Arrows at close range.
Genius Intellect: Stein is an extremely intelligent individual, being resourceful in the medical field and is considered brilliant though eccentric and unlicensed as well as various rumors surrounding him tinkering his own body and performing zombie experiments, eventually resurrecting Sid Barrett as a zombie. He's also knowledgeable in Soul Studies and even has knowledge on Magic and spells.
- Medical and Surgical Skills: According to Anya, Stein is a brilliant (but eccentric) unlicensed doctor. He's capable of performing advance, life-saving surgeries as well as treating and aid ailments caused by even Magic.
Soul Wavelength Attack Cancellation: Stein has stated himself that he can easily counter the attacks of certain Soul Wavelength attacks (such as Ultimate Move: Black☆Star Big Wave) by adjusting the characteristics of his Wavelength to match others, in which causes it to lose it's power. The relationship is similar to the Soul Resonance between that of a Meister and Weapon.
Spatial Sense: Stein's senses are even acute enough to be able to sense when space itself is being twisted.
Perhap's Stein's most well-known weakness is his sensitivity to Madness, having himself noted that he's especially sensitive to Asura's Madness Wavelength and even felt Arachne's Madness Wavelength even from the Czech Republic, despite being in Death City located in Nevada. This can cause him to have difficulty concentrating and always puts him at risk of losing his sanity.
During his battle with Medusa Gorgon, Spirit Albarn once noted that due to having not fought a serious opponent in a long time has caused him to "lose his edge" and also lost the ability to intimidate. Despite being a powerful Meister, he's still able to have trouble with high-caliber opponents like Medusa. He also admitted himself while his spar with Black☆Star that the assassin himself knows he can get just as "jammed up" as anyone else in regular hand-to-hand combat when he got distracted by the power of the latter's Soul Menace.
- Partnered with Spirit Albarn
Death Scythe (デス・サイズ, Desu Saizu): When partnered up with Spirit Albarn, Franken Stein has the capability of the usage of his Death Scythe transformation. Being extremely powerful and durable, the most critically acclaim of this transformation is Spirit's control of his Meister's Wavelength to make him much more powerful.
- Soul Thread Sutures ((魂糸縫合, Konshi Hōgō): After applying his Wavelength to his target via Soul Menace or it's variation, Stein is able to control the Wavelength within the body in which he's shot his Soul Menace into for a certain amount of time similar to that of a static charge. Due to the high level of precision and control required, it can only be performed by the most powerful of Meisters and Demon Weapons (such as Death Scythe). The suturing isn't limited onto to his target but even himself.
- Great Traditional Techniques of the Scythe-Meister (鎌職人伝統の大技, Kamashokunin dentō no ōwaza; FUNimation "Scythemeister Techniques of Lore"): Stein is capable of utilize one of the Great Technqiues typically used by Scythe-Meisters with extreme skill.
- Witch-Hunt (魔女狩り, Majogari; FUNimation "Witch Hunter"): Stein is able to perform and control one of the three Great Traditional Techniques of the Scythe-Meister. When applied during his skirmish with Medusa after defeating Crona, his Witch-Hunt was powerful enough to negate Medusa's Vector Arrow spell in one hit as well as Stein able to execute the technique almost instantaneously. It's assumed that it has the ability to profoundly act as a bane to Witches, Magic, Demons, and even Immortals.
- Experimental Ectoplasm (実験霊体, Jikken Reitai): This Soul Resonance special art allows Franken Stein with the usage of Death Scythe to create a large, globular spiritual body to protect him from incoming attacks where the body's composition is gelatinous. He used this Special Art to stop Crona/Ragnarok's Bloody Needle attack.
- Partnered with Marie Mjolnir
Demon Hammer Mjolnir (魔鎚•ミョルニル, Mattsui Myoruniru): When partnered up with Marie Mjolnir, Stein is extremely apt in making use of her demon weapon form. These capabilities include an unnamed Soul Resonance ability in which he can create pillars of intertwining energies from a triquetra symbol capable of killing Justin Law in one, single hit. A variation allows him to use only the triquetra symbol to kill multiple opponents. With this weapon on hand, he takes advantage of her Healing Wavelength to calm and have better control over his Madness.
- Lightning Rope (雷綱, Izuna): A hyper-nerve induction technique in which gives a Stein a massive boost to his physical capabilities by sending electrical pulses through the his motor nervous system, capable of acheiving speed and power that seemingly exceeds Justin Law's power.
- Lightning Rope-Madness State: When faced with overwhelming odds and partnered with the likes of Marie Mjolnir, Stein can release the cap of his Madness and enter an insane-like state. Within this state, his Madness and prowess is at such a state that Spirit Albarn exaggerated with a claim that his manner acts much like the Kishin himself. Appearance wise, much remains the same though he gains a notable long ovals of lights around where his glasses appears. This state lasts for as long as Lightning Rope is engaged. While in this state, he takes advantage of the speed granted to him by Mjolnir's Lightning Rope technique, combining such speeds with the ruthlessness in which rises from the released cap in Madness, ascending Stein to his full capability in fighting. Despite this release in Madness, however, Marie has asserted that he himself still has full capability in reasoning (with readers). Furthermore, he himself states that even in this state, he wouldn't allow himself to succumb to the effects of Madness for the sake of those he cares about.
- Partnered with Jacqueline O'Lantern Dupre
Demon Lamp (魔角灯, Ma Kakutō): Stein was once partnered up with Jacqueline O'Lantern Dupre in order to fend off the attacks of a Madness-induced Soul Eater. While using her, he was capable of using the chain to knock Soul off balance (although merely touching Soul's blade injured Jackqueline). Because of this, he resorted to handling the weapon backwards, allowing him to enhance his punches with the Demon Lamp's propulsion and increase the power of his punches.