The episodes follow pretty much the same format as the previous. There were 11-minute mysteries or a two-part episode.
Tropes Found in The New Scooby-Doo Mysteries:
- Accidental Hero: "A Night Louse at the White House" has Scooby's parents, Dada Doo and Mumsy Doo, accidentally incapacitate the episode's criminals by dropping Scooby's galoshes on their heads.
- Ageless Birthday Episode: "Happy Birthday, Scooby-Doo" is about Scooby's birthday and has no indication of how old he is now.
- Art Shift: "A Code in the Nose" through "The Nutcracker Scoob" used Hanna-Barbera's pioneering, but primitive, digital ink and paint system instead of the traditional method of shooting physically painted cels onto 35mm film. The downside, of course, is that these segments only exist in standard definition.
- The Bad Guy Wins: In "A Halloween Hassle in Dracula's Castle although Chandra is defeated, Igor is commended for his work of scaring the other monsters. This convinced them all to go back to their old jobs of being evil monsters prompting our gang to get the heck outta Dodge while they still can.
- Bad is Good and Good is Bad: In "A Halloween Hassle in Dracula's Castle", Igor turns out to have disguised himself as Van Helsing's ghost to scare the other monsters out of the castle so he'd never have to clean messes again. Being monsters, the others not only are not mad at Igor for his underhandedness, but even commend him for being so mean to them.
- The Bus Came Back: While only as guest stars, Fred and Velma appeared in several episodes in this series after being absent from the franchise since The Scooby-Doo and Scrappy-Doo Show. Fred became a mystery writer and Velma a NASA intern in their time away.
- Butt-Monkey: Pizza Louie's pizza delivery to the gang is repeatedly foiled by the Hand in "The Hand of Horror". The guy doesn't give up.
- Captain Ersatz: Thaddeus Blimp from "The Stoney Glare Stare" appears to have been inspired by the Marvel Comics villain the Kingpin. Both characters are bald, obese supervillains clad in white suits.
- Christmas Episode: "The Nutcracker Scoob", where Scooby, Shaggy, Scrappy, Daphne, and Fred put on a play for an orphanage and try to prevent the place from being shut down by Winslow Nickleby.
- Cyclops: The monster faced in "The Stoney Glare Stare" is a cyclops, who was really a scientist named Professor Miko disguising himself to aid Thaddeus Blimp.
- Elongating Arm Gag: One episode had Daphne restrain a fleeing Shaggy by extending her arms from offscreen.
- Expospeak Gag: Velma, as usual in "Happy Birthday, Scooby-Doo".Velma: The perpetrator may have used the superstructure's atmospheric control system to extricate himself!Scrappy: Which means the meanie probably hid in the vent!
- Expy: "A Halloween Hassle at Dracula's Castle" features Chandra the Unbelievably Remarkable (and Quite Interesting Too), a sorceress who performs as a stage magician; she's an expy of Zatanna, who happens to be the favorite character of the episode's writer, Paul Dini. Her name however is a deliberate Fridge Brilliance reference to radio character Chandu the Magician who fought monsters like Van Helsing did.
- Fun with Acronyms: One story features (and is named after) "Old MacDonald's Experimental Institute for Evolutionary Improvement of Organisms".
- Glass-Shattering Sound: Scooby is shown to have a destructive singing voice in "The 'Dooby Dooby Doo' Ado".
- Halloween Episode: "A Halloween Hassle in Dracula's Castle" has the gang find their way at a Halloween party attended by actual monsters and are hired to defeat the Ghost of Van Helsing.
- Harmless Villain: Cecil, the man behind the Mastermind disguise of the Man Behind The Curtain in Mission Un-Doo-Able is one of the least threatening villains in the series; for all his disguises, he runs away in fear and is a thin, pale man who the gang defeat easily.
- I Want My Mommy!: "A Night Louse at the White House" has Scooby cry "I want my Mumsy" when asked what he as to say in response to being mistaken for George Washington's ghost.
- Karma Houdini: The captain of the Delta Queen in the backstory of "Showboat Scooby". He stole Miss Magnolia's emerald necklace, thus causing her to leave his love rival, Colonel Beauregard, at the altar, and was never caught.
- Large and in Charge: Thaddeus Blimp in "A Stoney Glare Stare" is this kind of character. He's huge and is the big cheese.
- Let's Split Up, Gang!: Lampshaded in "Happy Birthday, Scooby-Doo" when Scooby recognizes Fred by his use of this catchphrase, and again in "Sherlock Doo":Shaggy: Like, which way? And don't tell me you want us to split up, Fred!Daphne: Sorry, Shaggy, we don't have much time! We've got to split up!Fred: Well, at least I didn't tell you.
- Mean Character, Nice Actor: In-Universe. Shaggy is cast as Scrooge in the play the gang puts on for the orphanage.
- Monster Mash: "A Halloween Hassle in Dracula's Castle" features the gang going to a party being thrown by Dracula for monsters.
- No Communities Were Harmed: The country of Klopstokia in "A Night Louse at the White House", whose ambassador and his wife were outed as a spies disguised as the ghosts of American historical figures, was a thinly-veiled jab at the Soviet Union. Considering how unflattering portrayals of Russians and/or Soviets was rife during the Reagan era (e.g. the Bolshevik scene in Annie and Drago in Rocky IV among others), this isn't surprising.
- Not-So-Forgotten Birthday: "Happy Birthday, Scooby-Doo" has Scrappy, Shaggy, and Daphne pretend to forget Scooby's birthday to prepare him for a surprise.
- Not Helping Your Case: Fred is being framed by Stuyvescent] as being the criminal sabotaging Scooby's birthday celebration. The real culprit does a pretty good job, and when the others (along with the policeman on the scene) voice their concerns, Fred panics and runs away, which naturally everyone finds even more suspicious.
- Private Detective: Though a few episodes still feature them as reporters, this season the gang mostly introduce themselves as the "Scooby-Doo Detective Agency" and are called in to investigate paranormal mysteries.
- "Scooby-Doo" Hoax: The gang facing monsters turning out to be criminals wearing disguises was once again present in this series as to be expected but sometimes also still averted by having the gang face real monsters.
- Shout-Out: "The Nutcracker Scoob" is filled with them for Christmas themes and the works of Charles Dickens. There's an old Scrooge-like miser who shares a last name with another Dickens character, his name being Winslow Nickleby. If the whole orphanage wasn't Dickensian enough for you, one of the kids is named Tiny Tina. Nickleby's cook being named Miss Muffinstuffer is meant to invoke some of Dickens' more silly naming conventions.
- Slapstick Knows No Gender: Velma gets a heck of a ride on a runaway broomstick during the Halloween Episode, crash landing in a bowl of punch.
- Theme Tune Roll Call:Come on, Scooby! Where ya been?
Trouble's on the loose again!
(Scooby...) They're not gonna get ya!
(Scooby-Doo...) Uh-uh! Scrappy's gonna help ya!
(Scooby...) Ooh, Shaggy's gonna be there!
(Scooby-Doo...) And Daphne, too!
- Van Helsing Hate Crimes: Parodied in "A Halloween Hassle in Dracula's Castle" where Dracula and the Wolfman are the victims and out to help the heroes. They are opposed by the Ghost of Van Helsing (one of the heroes from Dracula) and Chandra the magician (named after a heroic radio character who fought evil).
- We Need a Distraction: In "Ghosts of Ancient Astronauts", the gang has Scrappy taunt some guards into following him and lead them into the gang's trap.
- Yet Another Christmas Carol: The gang put on one for an orphanage in "The Nutcracker Scoob".