[13] Khanvilkar made her film debut in the Marathi comedy Golmaal (2006), in which she was paired opposite Bharat Jadhav and Jitendra Joshi, and her performance was well received.

Khanvilkar's biggest commercial success of that year was Zee Talkies' Saade Maade Teen, the remake of the 1958 Hindi film Chalti Ka Naam Gaadi.

[17] The next release was the supernatural horror film Phoonk, co-starring Sudeep, based on superstition and black magic, Khanvilkar's portrayal of a mature woman with a de-glamorized look was critically acclaimed.

[20] In 2009, Khanvilkar starred in Gaiir, a big budget Marathi suspense thriller film directed by Satish Rajwade which revolves around a newly married couple.

"[23] The film generated huge box office returns and she earned her first Best Actress nomination at Zee Chitra Gaurav Puraskar and Maharashtracha Favourite Kon.

[25] Khanvilkar's career prospects improved in 2010 when she gained widespread popularity for her Lavani performance in the song "Wajale Ki Bara" in Ravi Jadhav's film Natarang, which was sung by Bela Shende.

"[27] The song made her famous even in the interiors of Maharashtra, reviewer Chetana Panchal described her cameo as "impressive"[28] The same year, she reprised her role as Aarti in Phoonk 2.

Sonia Chopra of Sify noted her as "superb, especially when she's trying to convince Rajiv of the odd goings-on in the house,"[29] Komal Nahta of Koimoi.com wrote, "she does justice to her role and is very natural"[30] and DNA's Taran Adarsh found Khanvilkar's portrayal to be "expressive enough.

[37] Critic Ullhas Shirke wrote, "Khanvilkar, puts up an astounding emotion filled performance..." and further noted, "Her concern for the society is clearly noticed through her body language and spontaneous expressions.

Her first release was Baji, the first superhero film in Marathi, in which she played a fearless young girl who is the love interest of the titular character, portrayed by Shreyas Talpade.

[44] Next, she appeared in Welcome Zindagi, opposite Swapnil Joshi a dark comedy about life and death that was a Marathi remake of the Bengali film Hemlock Society.

"[46] In her next movie from the same year, she gained more recognition for her portrayal of Muslim girl Zareena, in Subodh Bhave's directorial feature film Katyar Kaljat Ghusali, which was based on the play of the same name.

[47] Khanvilkar's part required her to master the fine nuances of the Urdu language, which she achieved in pronunciation and diction with the help of her on-screen father, Sachin Pilagaonkar.

[63] Devesh Sharma of Filmfare opined, "Amruta don't have much to do really, other than looking pretty"[64] and Bollywood Hungama thought that Khanvilkar's talent was completely wasted and that's unfortunate considering that she just gave a memorable performance in Raazi.

[75] Next, Khanvilkar took on the role of the troubled Catholic wife of upright cop (played by Kunal Khemu) in Mohit Suri's action thriller Malang (2020), with several critics praising her performance with fewer words but a more expressive character.

"[79] The following year, she acted in the Marathi drama Well Done Baby (2021), which depicts the narrative of a modern young couple attempting to identify the purpose of their relationship while simultaneously dealing with the arrival of a new member into their life.

[81] In 2022, She next portrayed a downtrodden girl who never had the authority over her life decisions in Sachin Kundalkar's Pondicherry which was the first Marathi and one of the first Indian feature films to be shot completely on a smartphone.

"[83] Suyog Zore of Cinestaan called it as her best performance till now and wrote, "does a fine job as a woman who is finding it hard to come to terms with her mistake.

[86] Khanvilkar got her first titular role, as a tragic Tamasha performer in Prasad Oak's Marathi musical love drama Chandramukhi, based on Vishwas Patil's renowned novel of the same name.

[106] Next she also appeared in the Disney+ Hotstar action drama series Lootere, revolving around the intense narrative of a Ukrainian trading vessel hijacked by Somali pirates in international waters.

[107] Casts as the wife of a self-centered port president (played by Vivek Gomber), her character embarks on a journey to find her maid's missing son.

[117] She played a Marathi girl with big dreams and lofty aspirations, striving to achieve them through a questionable side hustle, set in the luxurious backdrop of Goa, she starred opposite Sharib Hashmi.

"[119][120] In addition to her Hindi projects, Khanvilkar starred in the Marathi film Like Aani Subscribe, a story tackling modern social media issues.

Sameer Ahire of Movie Talkies praised her performance, writing, "Khanvilkar springs a nice surprise as she plays a sophisticated and mature character, far from her glamorous image.

Mudit Bhatnagar of Times Now commended her for bringing "grace and depth" to the role,[124] while Santosh Bhingarde of Sakal described her portrayal as "brilliant," adding that "the tough and strong Maharani is played well by Amruta.

[126] On the occasion of Republic Day 2023, she announced a sports biopic on Lalita Shivaji Babar, an Indian long-distance runner from Satara district.

[151][152] Khanvilkar also participated as a contestant in Indian stunt reality serials Fear Factor: Khatron Ke Khiladi 10 and dance show Jhalak Dikhhla Jaa 10, where she ended up finishing in 8th and 9th place, respectively.

[159] On the occasion of Navratri 2022, she made her debut in singing by collaborating with the Abhanga Repost troupe on a Bharud song titled "Akkal Yeu De".

[162][163] In that very year, she released a devotional Ganpati song Ganaraj Gajanan under her banner Amritkala Studios, which was sung by National Award winner Rahul Deshpande.

[165] On 11 December 2024, she performed at the International Gita Mahotsav in Ujjain, alongside Adbhut Collective Arts, in a show titled "Tales of Krishna.