- Fitting with their personalities, anytime you return to the atelier with a new recipe book, Lydie sits and reads it studiously, while Sue sits next to her with a frown on her face.
- The regular Running Gag of Sue's fear of insects. The game uses any opportunity for this possible, including the comments made by the characters while exploring various areas, or if you make Sue herself capture insects using the Insect Net items.
- In another Running Gag, anytime that Pamela scares Sue with her status of being a ghost, to the point that Sue actually blocks the truth of it out of her mind.
- As usual, the Encyclopedia entries are all in-character and highly entertaining if you actually take the time to read them, and continue a number of running gags used throughout the game. For example, if you examine the Surf Bow weapon for Firis, she comments "This bow's designed to look like a wave. Its drawback is that it makes you hungry when you use it!" Lydie asks "Huh? Wait, you associate waves with fish?" and Sue replies "That's kind of a stretch... But this is Firis." Also, the above insect gag continues to any item even remotely associated with insects, such as the insect nets, which Sue will suggest you toss out. And each of the entries for actual insects comes with a Sue PSA, such as the one for the Comet Butterfly...Lydie: What a pretty butterfly! It's like a jewel! It's so sparkly, it just catches the eye! What would I have to eat to get wings like that?Sue: Sue PSA: Pretty bugs are still bugs, sorry!
- During their first visit to Etel Nepica, which is littered with memory fragments, Sue and Mathias see embarrassing moments from their childhoods. After this, they're seen praying at the sight of another memory fragment for an embarrassing memory from Alt to appear, unnerving Sophie. When the memory instead turns out to be that of Sophie and Firis's first meeting, Sue and Mathias are angrily calling for a do-over, mad that they got embarrassed while Sophie and Firis didn't.
- For Sophie's level 50 friendship event, Lydie and Sue walk in on Sophie doing maintenance on Plachta's doll body; as Sue screams in horror at Plachta's dismembered body and Lydie asks if Sophie committed a crime of passion, Plachta's head pipes up to admonish the girls:Plachta: She told you to wait out there. The two of you did this to yourselves, honestly.Lydie: S-She talked!Sue: Supernatural phenomena? Plachta is a ghost? Uwaaah, I can't take this!
- Late in the game, Lydie and Sue come across Sophie drinking with Corneria, and then Firis and Ilmeria drinking for the first time; the drunken antics of their seniors shocks them so much that they resolve to never drink once they come of age.
- At one point, Mathias comes to Firis's atelier to try and pick Sophie up; after Plachta and Firis get him to back off, he manages to offend Firis, who tells him she'd be game for a date, by telling her she's too young for him, which prompts Liane to pop up out of nowhere and personally run him out. He's never seen there again.
- After you fight Termina enough to draw out her true form, Termina, Maiden of the End, Suelle will talk about how all their fighting each other is just a way to deepen their friendship. Afterwards, each time you return for enough fight, Termina will talk about getting on with deepening the bonds of your friendship, followed by your immediately being cast into battle, with her declaring in battle "I'll show you hell!"
Funny / Atelier Lydie & Suelle: The Alchemists and the Mysterious Paintings