- At the start of this season, the nine-foot Jeopardy! logo changed its color from white to yellow. This remained in use until the end of the set's run in 1991.
- This is the first time that the show has taped for 230 half-hour episodes, rather than 195 half-hour episodes in the first two seasons. In this season only, a Coca-Cola byline is seen in the Merv Griffin Enterprises logo.
- Alex no longer enters with a microphone in his hand. So now, he has a clip-on microphone, but his podium still has a microphone, so Alex makes his entrance, and goes straight to the set.
- Starting with this season, Jeopardy! begins a long-standing tradition of making seasons consist of 46 weeks, and 230 half-hour episodes, which is starting on the second Monday in September and ending on the third Friday in July.
- The globe opening credits at the start of every episode changed its color to feature yellow Jeopardy! letters on a blue sphere with black lines divided into squares, rotating at warp speed. And then, it explodes to reveal the 1985-1991 set.
- Starting with this season, the contestants names appear onscreen in gold Korinna font. This remained in use until Season 12.
- The title cards for rounds and Daily Doubles changed its color to gold text on a silver background; the "DOUBLE" and "FINAL" in Double and Final Jeopardy!, as well as the Daily Double name, now use Gill Sans. For Video and Audio Daily Doubles, a navy-blue banner is featured with neither "VIDEO" nor "AUDIO" in white text, also using Gill Sans. On-screen displays of Daily Doubles and the Final Jeopardy! clue are now surrounded by blue backgrounds.
- This is the last season to feature Alex as the show's first producer. Starting in Season 4, George Vosburgh became the producer.
- The title cards that appear when the show went away and came back from commercial breaks are the same as last season.
- The primary color of the box displaying the contestants' Final Jeopardy! wagers and responses changed its color back to blue.
- During the 1986 Jeopardy! Tournament of Champions, the Merv Griffin Enterprises text is missing from the logo; all that appears below the griffin is "A Unit of The Coca-Cola Company", in red with the company name in Coca-Cola's proprietary script font and the rest of the text in Helvetica.
- After the 1986 Jeopardy! Tournament of Champions, the Merv Griffin Enterprises text returned and started to be shown between the Griffin and the Coca-Cola byline.
- For the 1986 Jeopardy! Tournament of Champions only, Johnny Gilbert's closing catchphrase is changed to "Jeopardy! is produced by Merv Griffin Enterprises, and it is distributed by KingWorld".s.
- In some episodes, the sponsor list and eligibility disclaimer appear in Helvetica font, while the closing credits still use Korinna.
- The copyright card is the same as in the later portions of Season 2.
- Season 3 of Jeopardy! kicks off on September 8, 1986.
- For the rest of the entire season, the blue coloration changes its color to teal, the lines are less pronounced, the letters are bolder, and the globe rotates at normal speed. A closed captioning bug is added to the opening credits. This lasted until the 1985-1991 set is retired in 1991 when the 1991-1996 set designed by Ed Flesh was used.
- The top and bottom light bands on the set flash during the introductions, just as it did since the previous season, in the first month, but the lights cease flashing after October 1986.
- The Tournament of Champions airs from November 10-21, 1986.
- The first Jeopardy! Tournament of Champions consists of 14 men and 1 woman Beryl Arbit.
- The first Jeopardy! Tournament of Champions is also the first Tournament of Champions to feature a distinct logo for the Tournament—featuring a bronze Jeopardy! logo on a silver banner, accompanied by light blue banners with gold text reading "$100,000" and "Tournament of Champions!", both in varying widths of Futura.
- On the November 13, 1986 episode, there is a funny blooper of ROMAN EMPIRE for $300, the clue being "By the 4th century A.D., Rome had 28 public ones stacked with rolls of papyrus" with Gary Giardina responding "What are Public Toilets?" causing laugher from Alex and the audience. After Harvey Becker gives the correct response of "What are Libraries?" Alex says he loves Gary's line for humor.
- On the November 14, 1986, episode, Chuck Forrest, who had the highest score in the regular competition, won the Tournament of Champions.
- On the February 2, 1987, episode, the KingWorld part of the closing catchphrase is slightly changed again to say "and is distributed by KingWorld".
- At some point between February 3, 1987, and the end of the season, the byline below the Merv Griffin Enterprises logo changes to "A unit of Coca-Cola TELEVISION", again using the proprietary Coca-Cola script font for the beverage brand's name.
- The first Jeopardy! Teen Tournament airs from February 16-27, 1987.
- Michael Galvin became the first champion to win $25,000.
- The first Jeopardy! Seniors Tournament airs from May 11-22, 1987.
- Zeke Sevilla Jr. became the first winner of the tournament.
- On the July 1, 1987 episode, Doug Molitor plays Final Jeopardy! all by himself.
- On the July 2, 1987 episode, the ending theme plays in it's full duration, ending during Johnny's catchphrase, and at the KingWorld Logo.
- Season 3 of Jeopardy! wraps up on July 24, 1987.
- Summer reruns air from July 27-September 4, 1987. Reruns later air from 1987-1988 on weekends in all markets (and weekdays in only some markets where season 4 airs in first-run). Reruns eventually air on Game Show Network in the late 1990s.