In 1999, the original titles were slated to be Clerks 2: Hardly Clerkin' and 'Clerks 2: Rude and Unwrapped'. Smith later modified the subtitle to Clerks II: The Passion Of The Clerks, lampooning the title of Mel Gibson's The Passion of the Christ. The film was originally scheduled for a 2005 release, and then a January 2006 release, but the production was pushed back due to other projects and Kevin Smith's involvement in the romantic comedy Catch and Release.

The film was shot on a single set in Buena Park, California, (right across the street from Knott's Berry Farm) and at the Quick Stop and R.S.T. Video stores in Leonardo, New Jersey, with some exceptions, the most notable being the go-kart scene, which was shot at Speedzone in City of Industry, California.

Smith released production diaries on the Clerks II website. They chronicle the entire making of the film from the first rehearsals all the way through to the final release. Some of these web diaries are also available on the two-disc DVD of the film. Smith released a Web-only teaser trailer on the Clerks II website on January 9, 2006, and a web-only trailer on April 2, 2006. Smith also released several shorts featuring action figures from his previous films to promote the film.

Before the release of the film, Kevin Smith had mentioned releasing an MP3 file commentary to be downloaded and listened to in movie theaters via iPod. Ultimately, theater owners and exhibitors objected[citation needed], and the plan was scrapped. The abandoned commentary, featuring Smith, Scott Mosier and Jeff Anderson, is included on the DVD.

The bookend Quick Stop scenes are in black and white (to simulate the original visual style of Clerks), while the rest of the film is in color. Smith has said that much of the film's color was desaturated almost to the point where the film had a similar texture to the first film. The contrast in color saturation used can be seen in the 'ABC sequence' in which a more vibrant and saturated color temperature is used to give a warm and sunny look that adds to the playful nature of the piece.

The film received generally mixed reviews from critics. At review aggregator website Rotten Tomatoes, reviews for Clerks II were split, with the film rated "fresh" overall (63% positive) but rated "rotten" by the website's top critics (55% positive).as of January 2009; the critical consensus was that the film "dishes up much of the graphic humor and some of the insight that made the 1994 original a cult hit". The Metacritic.com characterised the film's reception as "generally favourable", with metascore of 65 out of 100 from 29 reviews.