- Gotlib: In one of his cartoons Hamster Jovial tries to imitates Captain Beefheart's growly voice by singing "I'm Going To Booglarize You, Baby" from his album The Spotlight Kid" (1972), but throws up in the process. His girlfriend doesn't mind, since its "the gift itself that counts." Another cartoon makes Hamster Jovial strike a pose from the album cover of "The Spotlight Kid".
- Mutts: One gag had Frank make reference to three Beefheart songs "The Dust Blows Forward And The Dust Blows Back" and "Wild Life" from Trout Mask Replica and "Grow Fins" from The Spotlight Kid. 
- The Big Lebowski: "Her Eyes Are A Blue Million Miles" from Clear Spot is used on the soundtrack.
- In High Fidelity a desperate record collector wants to buy a copy of Safe as Milk, but Barry refuses to sell it to him, because he deems him unsuitable to own it. Eventually he just gives it away to a random client and fools him it's something totally else.
- In School of Rock (2003) is a scene where Dewey explains the different types of rock music and gives examples of famous groups and artists who represent the genre. He puts Frank Zappa in the category "?" branching off of Progressive Rock along with Can and Captain Beefheart.
- Frank Zappa's Uncle Meat references the line "Fast 'n' bulbous" from Trout Mask Replica inside the photos in the liner notes.
- In the Sex Pistols' song "New York" from Never Mind the Bollocks, Here's the Sex Pistols, Johnny Rotten references the song "Japan In A Dishpan" from Lick My Decals Off, Baby:Everybody knows Japan is a dishpan.
- The Tubes covered Beefheart's "My Head Is My Only House Unless It Rains" from "Clear Spot" on their album Now (1977).
- The band Dali's Car was named after the Beefheart song "Dali's Car" from Trout Mask Replica.
- The Fall covered "Beatle Bones 'N' Smokin' Stones" from Strictly Personal in 1996, available on The Complete Peel Sessions.
- The Belgian rock band dEUS references Beefheart a lot:
She's paintingOn my backA green tongueThe Beefheart one
- They sampled "The Blimp" from Trout Mask Replica on their debut single "Zea" (1992).
- During the song "W.C.'s First Draft" from their debut album Worst Case Scenario (1994) lead singer Tom Barman sings: "do the low yo yo" at one point, a reference to "Low Yo Yo Stuff" from Beefheart's "Clear Spot".
- "Roses" from In a Bar, Under the Sea also namedrops the musician:
- The 1996 song "Disappointed In The Sun" from The Ideal Crash (1998) was inspired by a quote from Beefheart in the 1993 documentary "Low Yo Yo Stuff" where he said he visited an exhibition by Vincent van Gogh and felt the colors where so great that when he left the museum and saw the sun he "felt disappointed".
- dEUS frontman Tom Barman and Guy Van Nueten also covered "Harry Irene" from Shiny Beast on their album "Live" (2002). During an interview in the Dutch talk show "Zomergasten" (2005) Barman said he respects Zappa's musical talent, but actually likes Captain Beefheart more.
- Sonic Youth: They covered "Electricity" from Safe as Milk on the tribute album "Fast 'N' Bulbous" in 1990.
- Coati Mundi covered "Tropical Hot Dog Night" from Shiny Beast on this album "The Former 12 Year Old Genius" (1983).
- Mark Lanegan covered "Clear Spot" from "Clear Spot" on "Here Comes That Weird Chill Beggars Banquet" (2003).
- The White Stripes covered "China Pig" from Trout Mask Replica, "Ashtray Heart" fromDoc at the Radar Station and "Party Of Special Things To Do" from Bluejeans & Moonbeams on their album "Party Of Special Things To Do" (2000).
- The Kills covered "Dropout Boogie" from Safe as Milk on their album "Keep On Your Mean Side" (2009).
- XTC covered "Ella Guru" from Trout Mask Replica in 1990.
- Joan Osborne covered "Her Eyes Are A Blue Million Eyes" from "Clear Spot" in 1996. The Black Keys also covered it in 2009.
- Stack Waddy covered "Sure Nuff 'N' Yes I Do" from Safe as Milk on their album "Dandelion" (1971).
- The Mock Turtles covered "Big Eyed Beans From Venus" from "Clear Spot" on the album "Fast N' Bulbous" (1988).
- PJ Harvey referenced Beefheart a few times:
- The line "don't you wish you never met her" from the Title Track of Rid of Me is a nod to a line from "Dirty Blue Gene" from Doc at the Radar Station.
- Her song "Meet Ze Monsta" from her album To Bring You My Love (1995) was inspired by the line "I'm playing this music/ so the young girls would come out/ to meet the monster tonight" from "Tropical Hot Dog Night" from Shiny Beast. The same song also uses the lines "You told her you love her/ so bring her to mother/ You love her, adapt her/ you love her, adapt her/ Adapt her, adapter/ adapt her, adapter" from Beefheart's "Drop-Out Boogie" from Safe as Milk (1967). The title track from that album also opens with "Well I was born in the desert, came on up from New Orleans", which is the same opening line from "Sure 'Nuff 'N' Yes I Do" from "Safe As Milk".
- PJ Harvey's music publishing company is called "Hot Head Music", after the track "Hot Head" from Doc at the Radar Station (1980).
- "Observatory Crest" from Bluejeans & Moonbeams has been covered by Whipped Cream note , Mercury Rev note and Snow Patrol note .
- Desert Island Discs: Hosts on the show who have chosen a track by Beefheart as one of their favorite musical records to bring to a deserted island are:
- John Lennon was a fan of Safe as Milk and was photographed once in his room with the Safe As Milk bumper stickers behind him. George Harrison had one too. .
- Courtney Love once claimed that she and Kurt Cobain had "great sex" while listening to Trout Mask Replica.
- Tom Waits credits his wife and musical collaborator Kathleen Brennan's introduction of Beefheart's music to him for his shift in musical style starting at around Swordfishtrombones. If Beefheart has a Spiritual Successor, it'd have to be Waits.