diff --git a/studio/frontend/src/features/recipe-studio/components/controls/layout-controls.tsx b/studio/frontend/src/features/recipe-studio/components/controls/layout-controls.tsx
index a4f039d6d1..3208688c04 100644
--- a/studio/frontend/src/features/recipe-studio/components/controls/layout-controls.tsx
+++ b/studio/frontend/src/features/recipe-studio/components/controls/layout-controls.tsx
@@ -5,6 +5,7 @@ import {
   useUpdateNodeInternals,
 } from "@xyflow/react";
 import { Button } from "@/components/ui/button";
+import { getFitNodeIdsIgnoringNotes } from "../../utils/graph/fit-view";
 
 type LayoutControlsProps = {
   direction: "LR" | "TB";
@@ -32,20 +33,29 @@ export function LayoutControls({
     requestAnimationFrame(() => {
       refreshNodeInternals();
       requestAnimationFrame(() => {
-        fitView({ duration: 250 });
+        fitView({
+          duration: 250,
+          nodes: getFitNodeIdsIgnoringNotes(getNodes()),
+        });
       });
     });
-  }, [fitView, onLayout, refreshNodeInternals]);
+  }, [fitView, getNodes, onLayout, refreshNodeInternals]);
 
   const handleToggleDirection = useCallback(() => {
     onToggleDirection();
     requestAnimationFrame(() => {
-      refreshNodeInternals();
+      onLayout();
       requestAnimationFrame(() => {
         refreshNodeInternals();
+        requestAnimationFrame(() => {
+          fitView({
+            duration: 250,
+            nodes: getFitNodeIdsIgnoringNotes(getNodes()),
+          });
+        });
       });
     });
-  }, [onToggleDirection, refreshNodeInternals]);
+  }, [fitView, getNodes, onLayout, onToggleDirection, refreshNodeInternals]);
 
   return (
     <Panel position="top-left" className="m-3 flex items-center gap-2">
diff --git a/studio/frontend/src/features/recipe-studio/components/controls/viewport-controls.tsx b/studio/frontend/src/features/recipe-studio/components/controls/viewport-controls.tsx
index 27e225f39e..e104841100 100644
--- a/studio/frontend/src/features/recipe-studio/components/controls/viewport-controls.tsx
+++ b/studio/frontend/src/features/recipe-studio/components/controls/viewport-controls.tsx
@@ -2,6 +2,7 @@ import { type ReactElement, useCallback } from "react";
 import { Lock, LockOpen, Maximize2, Minus, Plus } from "lucide-react";
 import { Panel, useReactFlow } from "@xyflow/react";
 import { Button } from "@/components/ui/button";
+import { getFitNodeIdsIgnoringNotes } from "../../utils/graph/fit-view";
 import { RECIPE_FLOATING_ICON_BUTTON_CLASS } from "../recipe-floating-icon-button-class";
 
 type ViewportControlsProps = {
@@ -13,7 +14,7 @@ export function ViewportControls({
   interactive,
   onToggleInteractive,
 }: ViewportControlsProps): ReactElement {
-  const { zoomIn, zoomOut, fitView } = useReactFlow();
+  const { zoomIn, zoomOut, fitView, getNodes } = useReactFlow();
 
   const handleZoomIn = useCallback(() => {
     zoomIn({ duration: 150 });
@@ -24,8 +25,11 @@ export function ViewportControls({
   }, [zoomOut]);
 
   const handleFitView = useCallback(() => {
-    fitView({ duration: 250 });
-  }, [fitView]);
+    fitView({
+      duration: 250,
+      nodes: getFitNodeIdsIgnoringNotes(getNodes()),
+    });
+  }, [fitView, getNodes]);
 
   return (
     <Panel position="bottom-left" className="m-3 flex items-center gap-2">
diff --git a/studio/frontend/src/features/recipe-studio/recipe-studio-page.tsx b/studio/frontend/src/features/recipe-studio/recipe-studio-page.tsx
index c83bd1fb28..f225dc2846 100644
--- a/studio/frontend/src/features/recipe-studio/recipe-studio-page.tsx
+++ b/studio/frontend/src/features/recipe-studio/recipe-studio-page.tsx
@@ -48,6 +48,7 @@ import type {
   RecipeNodeData,
 } from "./types";
 import { deriveDisplayGraph } from "./utils/graph/derive-display-graph";
+import { getFitNodeIdsIgnoringNotes } from "./utils/graph/fit-view";
 import { buildRecipePayload } from "./utils/payload";
 import type { RecipePayload } from "./utils/payload/types";
 import { buildDefaultSchemaTransform } from "./utils/processors";
@@ -370,7 +371,10 @@ export function RecipeStudioPage({
     let frame2 = 0;
     const frame1 = window.requestAnimationFrame(() => {
       frame2 = window.requestAnimationFrame(() => {
-        reactFlowInstance.fitView({ duration: 250 });
+        reactFlowInstance.fitView({
+          duration: 250,
+          nodes: getFitNodeIdsIgnoringNotes(reactFlowInstance.getNodes()),
+        });
       });
     });
     return () => {
@@ -421,7 +425,7 @@ export function RecipeStudioPage({
                 nodesDraggable={interactive}
                 nodesConnectable={interactive}
                 elementsSelectable={interactive}
-                fitView={true}
+                fitView={false}
                 className="h-full w-full rounded-t-none"
               >
                 <LayoutControls
diff --git a/studio/frontend/src/features/recipe-studio/stores/recipe-studio.ts b/studio/frontend/src/features/recipe-studio/stores/recipe-studio.ts
index 43dd42dcfa..3edb6cbb29 100644
--- a/studio/frontend/src/features/recipe-studio/stores/recipe-studio.ts
+++ b/studio/frontend/src/features/recipe-studio/stores/recipe-studio.ts
@@ -258,6 +258,12 @@ export const useRecipeStudioStore = create<RecipeStudioState>((set, get) => ({
   applyLayout: () =>
     set((state) => {
       const isTopBottom = state.layoutDirection === "TB";
+      const noteNodeIds = new Set(
+        Object.values(state.configs)
+          .filter((config) => config.kind === "markdown_note")
+          .map((config) => config.id),
+      );
+
       const displayGraph = deriveDisplayGraph({
         nodes: state.nodes,
         edges: state.edges,
@@ -266,7 +272,14 @@ export const useRecipeStudioStore = create<RecipeStudioState>((set, get) => ({
         auxNodePositions: {},
         llmAuxVisibility: state.llmAuxVisibility,
       });
-      const { nodes } = getLayoutedElements(displayGraph.nodes, displayGraph.edges, {
+      const layoutNodes = displayGraph.nodes.filter(
+        (node) => !noteNodeIds.has(node.id),
+      );
+      const layoutNodeIds = new Set(layoutNodes.map((node) => node.id));
+      const layoutEdges = displayGraph.edges.filter(
+        (edge) => layoutNodeIds.has(edge.source) && layoutNodeIds.has(edge.target),
+      );
+      const { nodes } = getLayoutedElements(layoutNodes, layoutEdges, {
         direction: state.layoutDirection,
         nodesep: isTopBottom ? 120 : 80,
         ranksep: isTopBottom ? 140 : 80,
@@ -275,6 +288,9 @@ export const useRecipeStudioStore = create<RecipeStudioState>((set, get) => ({
         nodes.map((node) => [node.id, node.position] as const),
       );
       const nextNodes = state.nodes.map((node) => {
+        if (noteNodeIds.has(node.id)) {
+          return node;
+        }
         const position = layoutedPositions.get(node.id);
         if (!position) {
           return node;
diff --git a/studio/frontend/src/features/recipe-studio/utils/graph/fit-view.ts b/studio/frontend/src/features/recipe-studio/utils/graph/fit-view.ts
new file mode 100644
index 0000000000..8b0175a1df
--- /dev/null
+++ b/studio/frontend/src/features/recipe-studio/utils/graph/fit-view.ts
@@ -0,0 +1,17 @@
+import type { Node } from "@xyflow/react";
+
+function isMarkdownNoteNode(node: Node): boolean {
+  if (node.type !== "builder") {
+    return false;
+  }
+  if (!node.data || typeof node.data !== "object") {
+    return false;
+  }
+  return (node.data as { kind?: string }).kind === "note";
+}
+
+export function getFitNodeIdsIgnoringNotes(nodes: Node[]): Array<{ id: string }> {
+  const nodesWithoutNotes = nodes.filter((node) => !isMarkdownNoteNode(node));
+  const targetNodes = nodesWithoutNotes.length > 0 ? nodesWithoutNotes : nodes;
+  return targetNodes.map((node) => ({ id: node.id }));
+}