Creative director Nicolas Guérin mentions that the game's stories are based on his own experiences of loss. He wanted to make a game that handled death in a way that felt more personal and intimate, referencing the loss of family and loved ones. The original concept had the game take place on a train instead of a boat, but the team decided that it did not really fit what they wanted.
Changing seasons were also discussed but then scrapped because the scope of putting that into the game was much too large and served little importance to the game as a whole. Farming sections were much larger too, putting the original concept closer to competing simulation games like Harvest Moon and Stardew Valley. Thunder Lotus made the decision to tone it back, making the resource collecting portions not as time consuming and setting it apart from those competitors.
The game is also padded with stories from the spirits that measure up to 90,000 words at the time GameSpot published the interview with Guérin on July 28, 2021. Guérin also mentioned doing research at end-of-life care facilities for a month as well as asking staff for Spiritfarer personal stories of loved ones to help flesh out the characters that were already in the works. The characters were designed first and then given raw personality traits, such as being attuned with their inner animal or more human in nature.
The game itself is described as a construct of Stella's mind and how she develops her views and understanding of death. Guérin mentions that this is also shown in the landscapes of the islands as the game flows and Stella travels the map.