The second season of the American adult animated television series Star Trek: Lower Decks is set in the 24th century and follows the adventures of the low-ranking officers with menial jobs on the starship Cerritos, one of Starfleet's least important starships. The season was produced by CBS Eye Animation Productions in association with Secret Hideout, Important Science, Roddenberry Entertainment, and animation studio Titmouse, with Mike McMahan serving as showrunner and Barry J. Kelly as supervising director.

Tawny Newsome, Jack Quaid, Noël Wells, and Eugene Cordero voice the lower decks crew members of the Cerritos, with Dawnn Lewis, Jerry O'Connell, Fred Tatasciore, and Gillian Vigman providing voices for the ship's senior officers. Lower Decks was ordered for two seasons in October 2018 with McMahan on board as showrunner. Production took place remotely due to the COVID-19 pandemic and some of the season's writers did not meet in person while working on it. The season continues some overarching storylines from the first season, such as the threat of the Pakleds and the relationship between Beckett Mariner (Newsome) and her mother, Captain Carol Freeman (Lewis). Titmouse began work in August 2020. The season features many connections and references to past Star Trek media such as Star Trek: The Next Generation, including several actors returning as guest stars.

The season premiered on the streaming service Paramount+ on August 12, 2021, and ran for 10 episodes until October 14. It received positive reviews from critics, who felt it was a confident continuation that improved on the first season. This was despite concerns about the large number of Star Trek references and some criticisms of the season's sexual content. The penultimate episode, "wej Duj", was considered by some critics to be the best of the series and was nominated for a Hugo Award. A third season was ordered in April 2021.

CBS All Access officially ordered two seasons of Star Trek: Lower Decks in October 2018. Mike McMahan was set as showrunner for the series. By late March 2020, work on the series was taking place remotely due to the COVID-19 pandemic forcing staff to work from home. Executive producer Alex Kurtzman said in August that work on the season was "barreling ahead, full steam ahead", and had not been delayed by the pandemic unlike the live-action Star Trek series Discovery, Picard, and Strange New Worlds. A month later, ViacomCBS announced that CBS All Access would be expanded and rebranded as Paramount+ in March 2021. The season's third episode, "We'll Always Have Tom Paris", is the 800th Star Trek episode produced for television.

Writing for the second season began by March 2020, and was completed by mid-September. Due to the pandemic, the whole season was written remotely using Zoom and some new writers did not meet the others in person while working on the season. It was written knowing that fans would be able to stream the first two seasons back-to-back; McMahan wanted to carry the energy of the first season's final three episodes into the start of the second season, feeling that those episodes were when the writing team settled into the right approach for the series. Because the second season was mostly written before the first was released, the writers were not able to take fan responses into account and had to trust that the first season would be positively received.

McMahan said the second season would combine standalone episodes with season-long character arcs, and would take inspiration from the storytelling of Star Trek: Voyager and Star Trek: Deep Space Nine in addition to that of Star Trek: The Next Generation. He said many members of the crew had seen all of the previous Star Trek series, but they revisited specific episodes together. This included the Star Trek: The Original Series episode "A Private Little War", which introduced the alien Mugatos. Writer Ben Rodgers "could not get over" the inconsistent pronunciation of "Mugato" in the episode, a production mistake that the Lower Decks team wanted to celebrate, so the episode "Mugato, Gumato" has a running joke about the different pronunciations. McMahan said the second season would not undo the end of the first, which saw Brad Boimler working on the USS Titan. He compared this to storylines on the series Farscape which took its characters away from the main starship. Other elements that were left for the second season include Sam Rutherford's memory issues, Beckett Mariner working with her mother Captain Carol Freeman, and the Pakleds being a threat. McMahan wanted to address LGBT characters and relationships better than in the first season, especially by more explicitly depicting Mariner as bisexual.

The writers had a mandate from McMahan for the season to elevate the characters D'Vana Tendi and Sam Rutherford so they were true co-leads of the series alongside Mariner and Boimler. He wanted to explore new character combinations, such as telling a story with Mariner and Tendi together, which some critics had called for after they did not have any episodes together in the first season. The pair go on a mission together in "We'll Always Have Tom Paris", in which the characters make a joke acknowledging that it was a "glaring omission" for them to have not teamed-up before then. The episode's title is a reference to the Next Generation episode "We'll Always Have Paris", which itself was a reference to the line "We'll always have Paris" from the film Casablanca (1942). McMahan also wanted some episodes to focus on supporting characters such as Dr. T'Ana and chief engineer Billups—the latter being a "secret sleeper favorite" character for the writers. He was wary of changing the main characters so much that they got too close to characters and storylines that previous Star Trek series had already covered, and hoped to develop the main characters across the seasons without departing too much from the central premise of the series. An underlying theme for the season is the characters learning to trust each other, and it ends with Mariner successfully opening up to her mother. Freeman begins the season feeling that she should move up to "bigger and better places", but learns by the finale that she is in the right place on the Cerritos. That is another underlying theme for the season, which Freeman voices with the line "the carpets are greyer on the other side of the ship". Boimler has a similar journey in the season, wanting to be on the Titan but ending up happy to rejoin the Cerritos. Freeman's arc connects to the season-long Pakled story, which ends with her being arrested for apparently destroying the Pakled homeworld. This ends the season on a cliffhanger, setting up a new character arc for Mariner in the third season. Late in production on the finale, McMahan realized that this cliffhanger should include the "To Be Continued..." title card that previous Star Trek series used.

McMahan hoped to replicate the success of the first season's last three episodes by again having a sketch comedy episode ("I, Excretus"), a penultimate episode that breaks form for the series ("wej Duj"), and a big finale ("First First Contact"). The idea of "wej Duj", which means "Three Ships" in the Klingon language, came from the writers wanting to do something that had not been seen before and being surprised to learn that no previous series had told a contained story on a Vulcan ship. The episode shows "more lower decks than ever before" by exploring lower decks crew on the Cerritos, a Vulcan ship, and a Klingon ship. McMahan said this was the kind of story he would pitch if given the opportunity to make a Star Trek film, and described the episode as a "triple-mini-movie that's part [Star Trek VI: The Undiscovered Country (1991)], part this Vulcan thing we've never seen before", and also ties-into the season-long Pakled storyline. One element that he was not able to include, due to logistics, was having the full opening credits written in alternating Vulcan and Klingon text, but he was able to have the episode title shown in Klingon characters. This was a first for the franchise. For the finale, McMahan wanted a big moment that did not involve crashing the ship since that had already been done many times before in the franchise. Instead, for the first time in Star Trek, the hull plating is stripped from the whole ship. This was inspired by debris getting stuck in the hull of the USS Enterprise in the Star Trek: Enterprise episode "Minefield". The finale also introduces Cetacean Ops, an area of the starship for water-based crewmembers. It was first mentioned in the Next Generation episodes "Yesterday's Enterprise" and "The Perfect Mate" and was detailed in the Star Trek: The Next Generation Technical Manual by Rick Sternbach and Michael Okuda, but was never shown in that series due to the budgetary and logistical limitations of 1980s television. McMahan said it was a life-long dream come true to finally see Cetacean Ops on screen.