I am writing a story and I'm stuck in doing a form of transition.

Basically, Fluttershy was..uh, unconscious by something earlier and the first chapter is recounting the event before that happened. Then at the end of the chapter, she was cowering in fear (in the flashback) with eyes closed. She heard footsteps walking towards her and spoke to her. Like this:

"Move! Out of the boat!" The soldiers obeyed the unicorn. The steps and chatter were audible to Fluttershy, who were still quivering in fear. Her breath was shaky and her hands were still tightly against her ears.

Then, she heard footsteps coming towards her. She felt a poke by someone's boot.

"Get out, quick!"

I want the chapter to stop there. Then, Fluttershy will awake as if she was startled in the next chapter. I want to make it, you know, less jarring.

Why? That seems perfectly fine to me.

6625039
So to clarify, the part you quoted is the end of one chapter, then the start of the next is when she wakes up with a jolt? If that’s the case, then I agree this is kind of jarring. The main problem is nothing establishes that Fluttershy was knocked out. Extending it just a couple of sentences would make the transition much better.

"Move! Out of the boat!" The soldiers obeyed the unicorn. The steps and chatter were audible to Fluttershy, who was still quivering in fear. Her breath was shaky and her hands were still tightly against her ears.

Then, she heard footsteps coming towards her. She felt a poke by someone's boot.

"Get out, quick!"

Unable to find the willpower to obey, Fluttershy just shut her eyes tighter.

“Fine, you asked for it.”

There was the sound of movement, and the next thing Fluttershy was aware of was a sudden pain to the back of her head. Then, everything faded away.

Obviously just an example since I don’t know what’s happening in your story, but yeah, something like that. Establish the knock out so that when readers start the next chapter and see her waking up, they know why she’s waking up.

(Also, minor thing, you said “to Fluttershy, who were still quivering” when it should be “who was still quivering”)

6625073
Really?

6625174
Well, it's not she was knocked out right there. It happened later. Like there is a gap between that line being told to Fluttershy and her waking up.

Yes. Really. Anything you do to make it less is taking away your chapter end. You'll add anything from a paragraph to a page more. If that is acceptable to you, then continue the scene until she gets knocked out, and that becomes your chapter end. If not, then accept that your chapter end will be abrupt.