Bonnie is a very powerful witch, as well as one of the most powerful witches of her family lineage seen. Having discovered her heritage in a relatively short time prior, her powers have developed exponentially throughout the series. Within the span of at least two years, she transformed from a simple novice in the art of witchcraft to a nearly unstoppable force capable of taking down the oldest and most powerful supernatural creatures as well as controlling nature to a great extent. This could be attributed to the fact that she descended from a line of powerful Bennett witches that begun with Qetsiyah, an extremely powerful witch responsible for creating the Immortality Spell.
As a Bennett witch, a direct descendant of Qetsiyah and the member of an extremely powerful bloodline of witches, there are a few spells limited to her bloodline. Due to being related to Qetsiyah, the creator of the Other Side, only a Bennett witch such as herself can drop the Veil to the Other Side. The same applied to the tomb in which Silas was buried, as only a Bennett witch could open it. Malachai's prison too was created by a Bennett witch, therefore, Bonnie was the only one who could give him an escape.
After being freed from the vampire-huntress spell transferred to her by Rayna and the shaman, Bonnie's magic did not resurface for unknown reasons, which left her temporarily disempowered.
Bonnie is the only witch on the show to have participated in the creation of two different dimensions, having created a psychic afterlife dimension through her latent psychic abilities and a magical Prison World rooted in Gemini magic by empowering the siphoner witches Lizzie and Josie Saltzman and aiding them in their spell.
After the traumatic death of Enzo, Bonnie sent out a powerful blast that awakened her psychic powers. Originally, Bonnie had thought that she was a psychic in Pilot, however, it turned out that she was a witch.
At the point of Enzo's death and the psychic blast, Bonnie also created an alternate-dimension, a feat that nobody, according to Arcadius, had accomplished in four thousand years since he himself accomplished said feat. Following this creation, Bonnie was able to deprive Arcadius of Enzo's soul, accidentally sending his soul to her alternate-dimension instead.
Bonnie also showed that she has competent psychic links with people. She was able to, on multiple accounts, sense where people were and events regarding Cade. She also had a strong mental link with Elena, which allowed her to sense when she was in danger. However, it is unknown if this is because of the direct life-link placed upon their lives by Malachai Parker.
Due to the psychic link from her personal dimension, she and she-alone had the ability to see Enzo's spirit, as he was hidden from Arcadius. Like Cade, she too could see spirits that lingered in limbo, or the In-between, such as when Damon died but his spirit had not yet been claimed by Arcadius. Upon similar occasions, after Bonnie let go of Enzo and the link from her dimension, she briefly died, her heart having stopped due to being overwhelmed from reclaiming her magic, and reunited with both Elena and Enzo. Elena was described as "dead", or a "spiritual coma", and Enzo having found peace appear to her and informed her it was not yet her time to die. While protecting Mystic Falls, both Enzo and the spirits of Bonnie's ancestors appeared to her; all spirits that had previously found peace. It remains unclear as to whether this was due in part to her psychic abilities or the result of the spirits themselves. Despite this interaction, Bonnie did not express the ability to see Enzo after his spirit continued to watch over her as she packed to travel the world.
After returning from the Other Side with Qetsiyah's help, Bonnie had the ability to interact with those in the mortal plane and the supernatural purgatory. However, she was stuck with having to deal with the recently deceased supernatural creatures that have to pass through her to get to the Other Side. Through a powerful and complex spell, she was capable of bringing the denizens of the Other Side back into the mortal plane through physical contact. However, when the spell is interrupted and stopped entirely, she loses this ability.
Upon receiving Rayna Cruz's last life, and becoming the supernatural Huntress, Bonnie gained new abilities. The most prominent ability Bonnie gained was enhanced strength, even more so than that of Rayna before her and any vampire, including the Originals.
As the Huntress' abilities are tied to the phoenix sword, Bonnie was able to track any victim that she had stabbed with the sword, including being able to get inside their head. Bonnie also gained a longer lifespan, with her aging slowed, however, she did not inherit Rayna's gift of self-ressurection due to the harnessing of Rayna's last life.
Although Bonnie lost the ability to practice magic before becoming the Huntress, her ability to do so did not return, and she was unable to use magic to her advantage, however, she did gain the ability of being immune to magic, much like her predecessor.
With the Eight Everlastings all deceased, Bonnie lost the abilities afforded to her through her status as the Huntress.