Since then he has appeared in many films with mixed success throughout the late 1980s and 1990s. Most of his films where he had the leading role did not fare well at the box office from 1992. In most films, he was cast as the second lead to senior actors like Rajesh Khanna, Dharmendra, Jeetendra, Sunny Deol and Sanjay Dutt. Some of those hit films with him in second lead, are Paap Ki Duniya (1988), Khatron Ke Khiladi (1988), Ghar Ka Chiraag (1989), Nakabandi, Zahreelay (1990), Rupaye Dus Karod, Vishwatma (1992), Lootere (1993) and Aankhen (1993). His solo hit was Parda Hai Parda (1992 film).

Chunky Pandey worked as an instructor in acting school in 1986. He used to be senior to many junior budding artistes such as Akshay Kumar.

Pandey debuted his acting career with the 1987 multi-starer film Aag Hi Aag opposite Neelam Kothari. Film Producer Pahlaj Nihalani gave Chunky Pandey his first break in 1987 by signing him up for two films:- his debut film and Paap Ki Duniya. He got his second successful film Paap Ki Duniya with Sunny Deol and Neelam. Subsequently, Pandey appeared in many multi-hero films from 1987 to 1993. In 1988, Pandey was appreciated for his supporting role in N. Chandra's movie Tezaab featuring Anil Kapoor and Madhuri Dixit. Pandey played the character of Babban, Munna's (Anil Kapoor) friend. For his performance in Tezaab, Pandey was nominated for the Filmfare Award for the Best Supporting Actor.

The advent of the 1990s saw a new wave of actors like Aamir Khan, Salman Khan and Shahrukh Khan taking on roles as "romantic heroes", while Ajay Devgan, Akshay Kumar and Suniel Shetty grabbed the "action hero" roles. Pandey found it difficult to slot himself in either category. In addition, by the late nineties, solo-hero films were back in vogue instead of the multi-hero films in which Pandey was generally cast.

Chunky grew increasingly tired of playing second fiddle to more prominent actors, but had difficulty being seen as marketable, other than supporting household names. "I was offered hero ke bhai ka (lead actor's brother) roles," Chunky said. "I (told them), 'Boss, not happening.'" He moved to act as hero in Bangladesh films. In 1995, he was offered his first films as the lead hero in Bangladeshi films. He acted in six films between 1995 and 1997 as hero in Bangladesh and all of them were successful. However he got no films at all in Bollywood between 1997 and 2002.

Chunky Pandey returned to Bollywood in 2003 playing minor supporting roles in Qayamat: City Under Threat, Elaan, Don: The Chase Begins Again and Apna Sapna Money Money.

In 2005, Pandey was critically acclaimed for his dark role as an underworld gangster in the Ram Gopal Varma film D – Underworld Badshah. Later, Director Ram Gopal Varma roped him in for Darwaaza Bandh Rakho, a dark comedy thriller in which he played one of four Robbers who hold a family hostage.

Pandey has played the role of the Indo-Italian "Aakhiri Pasta" in the 2010 comedy hit Housefull followed by his reprised roles in the sequels Housefull 2 in 2012, and in Housefull 3 in 2016.