Activate the starter. Feed your sourdough starter and allow it to become active and bubbly before making the dough.
Make the dough. Add the active sourdough starter, filtered water, honey, and sea salt to the bowl of an electric mixer. Mix until combined, then add the bread flour.
Rest the dough. Let the dough rest for 10 minutes.
Knead. Using the dough hook attachment, knead on low speed for about 7 minutes, until the dough is smooth and firm. If adding mix-ins, add them during the final minute of kneading.
Let the dough rise overnight. Cover the dough and allow it to rise for approximately 10–12 hours, or until roughly doubled in size.
Shape the bagels. Divide the dough into 135-gram portions and shape each portion into a ball. Press your thumb through the center and gently stretch the opening to form a bagel shape.
Second rise. Place the shaped bagels on a parchment-lined baking sheet, cover, and allow them to rise for approximately 2 hours.
Boil the bagels. Bring a large pot of water to a boil. Add 3–4 bagels at a time and boil for 2 minutes per side. Carefully remove them and transfer to a parchment-lined baking sheet.
Add toppings. While the bagels are still damp from the water bath, add or dip them into your desired toppings.
Bake. Bake at 400°F for 22–26 minutes, or until golden brown.