diff --git a/src/features/boulder-state/storage.test.ts b/src/features/boulder-state/storage.test.ts
index 4bced7abc..65f6ad87e 100644
--- a/src/features/boulder-state/storage.test.ts
+++ b/src/features/boulder-state/storage.test.ts
@@ -433,63 +433,89 @@ describe("boulder-state", () => {
   })
 
   describe("getPlanProgress", () => {
-    test("should count completed and uncompleted checkboxes", () => {
-      // given - plan file with checkboxes
+    test("should count only top-level tasks under TODOs and Final Verification Wave sections", () => {
+      // given - plan with top-level tasks in tracked sections
       const planPath = join(TEST_DIR, "test-plan.md")
       writeFileSync(planPath, `# Plan
-- [ ] Task 1
-- [x] Task 2  
-- [ ] Task 3
-- [X] Task 4
+
+## TODOs
+- [ ] 1. Task 1
+- [x] 2. Task 2
+- [ ] 3. Task 3
+- [X] 4. Task 4
+
+## Final Verification Wave
+- [ ] F1. Final review
 `)
 
       // when
       const progress = getPlanProgress(planPath)
 
       // then
-      expect(progress.total).toBe(4)
+      expect(progress.total).toBe(5)
       expect(progress.completed).toBe(2)
       expect(progress.isComplete).toBe(false)
     })
 
-    test("should count space-indented unchecked checkbox", () => {
-      // given - plan file with a two-space indented checkbox
-      const planPath = join(TEST_DIR, "space-indented-plan.md")
+    test("should ignore nested Acceptance Criteria checkboxes under TODOs (issue #3066)", () => {
+      // given - plan with 9 completed top-level tasks and unchecked nested acceptance criteria
+      const planPath = join(TEST_DIR, "issue-3066-plan.md")
       writeFileSync(planPath, `# Plan
-  - [ ] indented task
+
+## TODOs
+- [x] 1. Implement feature A
+
+  **Acceptance Criteria**
+  - [ ] criterion 1
+  - [ ] criterion 2
+
+- [x] 2. Implement feature B
+
+  **Acceptance Criteria**
+  - [ ] criterion 3
+  - [ ] criterion 4
+
+- [x] 3. Implement feature C
+- [x] 4. Implement feature D
+- [x] 5. Implement feature E
+- [x] 6. Implement feature F
+- [x] 7. Implement feature G
+- [x] 8. Implement feature H
+- [x] 9. Implement feature I
+
+## Final Verification Wave
+- [ ] F1. Final review
 `)
 
       // when
       const progress = getPlanProgress(planPath)
 
       // then
-      expect(progress.total).toBe(1)
-      expect(progress.completed).toBe(0)
+      expect(progress.total).toBe(10)
+      expect(progress.completed).toBe(9)
       expect(progress.isComplete).toBe(false)
     })
 
-    test("should count tab-indented unchecked checkbox", () => {
-      // given - plan file with a tab-indented checkbox
-      const planPath = join(TEST_DIR, "tab-indented-plan.md")
+    test("should ignore checkboxes outside TODOs and Final Verification Wave sections", () => {
+      // given - plan with checkboxes in Work Objectives, Success Criteria, and other sections
+      const planPath = join(TEST_DIR, "ignore-other-sections-plan.md")
       writeFileSync(planPath, `# Plan
-	- [ ] tab-indented task
-`)
 
-      // when
-      const progress = getPlanProgress(planPath)
+## Work Objectives
 
-      // then
-      expect(progress.total).toBe(1)
-      expect(progress.completed).toBe(0)
-      expect(progress.isComplete).toBe(false)
-    })
+### Definition of Done
+- [ ] Verifiable condition with command
 
-    test("should count mixed top-level checked and indented unchecked checkboxes", () => {
-      // given - plan file with checked top-level and unchecked indented task
-      const planPath = join(TEST_DIR, "mixed-indented-plan.md")
-      writeFileSync(planPath, `# Plan
-- [x] top-level completed task
-  - [ ] nested unchecked task
+## TODOs
+- [x] 1. Real task one
+- [ ] 2. Real task two
+
+## Success Criteria
+
+### Final Checklist
+- [ ] All Must Have present
+- [ ] All Must NOT Have absent
+- [ ] All tests pass
 `)
 
       // when
@@ -501,11 +527,14 @@ describe("boulder-state", () => {
       expect(progress.isComplete).toBe(false)
     })
 
-    test("should count space-indented completed checkbox", () => {
-      // given - plan file with a two-space indented completed checkbox
-      const planPath = join(TEST_DIR, "indented-completed-plan.md")
+    test("should ignore indented checkboxes under top-level tasks", () => {
+      // given - plan with indented unchecked nested checkboxes
+      const planPath = join(TEST_DIR, "nested-indented-plan.md")
       writeFileSync(planPath, `# Plan
-  - [x] indented completed task
+
+## TODOs
+- [x] 1. top-level completed task
+  - [ ] nested unchecked task
 `)
 
       // when
@@ -517,20 +546,67 @@ describe("boulder-state", () => {
       expect(progress.isComplete).toBe(true)
     })
 
-    test("should return isComplete true when all checked", () => {
-      // given - all tasks completed
-      const planPath = join(TEST_DIR, "complete-plan.md")
+    test("should require proper task label format in TODOs", () => {
+      // given - plan with malformed labels (no numeric prefix)
+      const planPath = join(TEST_DIR, "malformed-labels-plan.md")
       writeFileSync(planPath, `# Plan
-- [x] Task 1
-- [X] Task 2
+
+## TODOs
+- [ ] no number prefix
+- [x] 1. Valid numbered task
 `)
 
       // when
       const progress = getPlanProgress(planPath)
 
       // then
-      expect(progress.total).toBe(2)
+      expect(progress.total).toBe(1)
+      expect(progress.completed).toBe(1)
+      expect(progress.isComplete).toBe(true)
+    })
+
+    test("should require F-prefix label format in Final Verification Wave", () => {
+      // given - plan with malformed final-wave labels
+      const planPath = join(TEST_DIR, "malformed-final-plan.md")
+      writeFileSync(planPath, `# Plan
+
+## TODOs
+- [x] 1. Implementation done
+
+## Final Verification Wave
+- [ ] missing F-prefix
+- [ ] F1. Proper final review
+- [x] F2. Another final review
+`)
+
+      // when
+      const progress = getPlanProgress(planPath)
+
+      // then
+      expect(progress.total).toBe(3)
       expect(progress.completed).toBe(2)
+      expect(progress.isComplete).toBe(false)
+    })
+
+    test("should return isComplete true when all top-level tasks checked", () => {
+      // given - all top-level tasks completed
+      const planPath = join(TEST_DIR, "complete-plan.md")
+      writeFileSync(planPath, `# Plan
+
+## TODOs
+- [x] 1. Task 1
+- [X] 2. Task 2
+
+## Final Verification Wave
+- [x] F1. Final review
+`)
+
+      // when
+      const progress = getPlanProgress(planPath)
+
+      // then
+      expect(progress.total).toBe(3)
+      expect(progress.completed).toBe(3)
       expect(progress.isComplete).toBe(true)
     })
 
@@ -555,6 +631,25 @@ describe("boulder-state", () => {
       expect(progress.total).toBe(0)
       expect(progress.isComplete).toBe(true)
     })
+
+    test("should support asterisk bullet top-level tasks", () => {
+      // given - plan with asterisk bullet tasks
+      const planPath = join(TEST_DIR, "asterisk-bullet-plan.md")
+      writeFileSync(planPath, `# Plan
+
+## TODOs
+* [x] 1. Task using asterisk bullet
+* [ ] 2. Another asterisk task
+`)
+
+      // when
+      const progress = getPlanProgress(planPath)
+
+      // then
+      expect(progress.total).toBe(2)
+      expect(progress.completed).toBe(1)
+      expect(progress.isComplete).toBe(false)
+    })
   })
 
   describe("getPlanName", () => {
diff --git a/src/features/boulder-state/storage.ts b/src/features/boulder-state/storage.ts
index 0b3eefe54..f72a57037 100644
--- a/src/features/boulder-state/storage.ts
+++ b/src/features/boulder-state/storage.ts
@@ -196,8 +196,25 @@ export function findPrometheusPlans(directory: string): string[] {
   }
 }
 
+const TODO_HEADING_PATTERN = /^##\s+TODOs\b/i
+const FINAL_VERIFICATION_HEADING_PATTERN = /^##\s+Final Verification Wave\b/i
+const SECOND_LEVEL_HEADING_PATTERN = /^##\s+/
+const UNCHECKED_CHECKBOX_PATTERN = /^(\s*)[-*]\s*\[\s*\]\s*(.+)$/
+const CHECKED_CHECKBOX_PATTERN = /^(\s*)[-*]\s*\[[xX]\]\s*(.+)$/
+const TODO_TASK_PATTERN = /^\d+\.\s+/
+const FINAL_WAVE_TASK_PATTERN = /^F\d+\.\s+/i
+
+type ProgressSection = "todo" | "final-wave" | "other"
+
 /**
  * Parse a plan file and count checkbox progress.
+ *
+ * Only top-level (zero-indent) checkboxes under `## TODOs` and
+ * `## Final Verification Wave` sections are counted. The checkbox
+ * body must carry a valid task label (`N.` for TODOs, `FN.` for
+ * Final Verification Wave). Nested acceptance-criteria checkboxes
+ * and checkboxes in other sections are intentionally ignored so
+ * that progress tracking stays aligned with `readCurrentTopLevelTask`.
  */
 export function getPlanProgress(planPath: string): PlanProgress {
   if (!existsSync(planPath)) {
@@ -206,13 +223,47 @@ export function getPlanProgress(planPath: string): PlanProgress {
 
   try {
     const content = readFileSync(planPath, "utf-8")
-    
-    // Match markdown checkboxes: - [ ] or - [x] or - [X]
-    const uncheckedMatches = content.match(/^\s*[-*]\s*\[\s*\]/gm) || []
-    const checkedMatches = content.match(/^\s*[-*]\s*\[[xX]\]/gm) || []
+    const lines = content.split(/\r?\n/)
+    let section: ProgressSection = "other"
+    let total = 0
+    let completed = 0
 
-    const total = uncheckedMatches.length + checkedMatches.length
-    const completed = checkedMatches.length
+    for (const line of lines) {
+      if (SECOND_LEVEL_HEADING_PATTERN.test(line)) {
+        section = TODO_HEADING_PATTERN.test(line)
+          ? "todo"
+          : FINAL_VERIFICATION_HEADING_PATTERN.test(line)
+            ? "final-wave"
+            : "other"
+        continue
+      }
+
+      if (section !== "todo" && section !== "final-wave") {
+        continue
+      }
+
+      const checkedMatch = line.match(CHECKED_CHECKBOX_PATTERN)
+      const uncheckedMatch = checkedMatch ? null : line.match(UNCHECKED_CHECKBOX_PATTERN)
+      const match = checkedMatch ?? uncheckedMatch
+      if (!match) {
+        continue
+      }
+
+      if (match[1].length > 0) {
+        continue
+      }
+
+      const taskBody = match[2].trim()
+      const labelPattern = section === "todo" ? TODO_TASK_PATTERN : FINAL_WAVE_TASK_PATTERN
+      if (!labelPattern.test(taskBody)) {
+        continue
+      }
+
+      total++
+      if (checkedMatch) {
+        completed++
+      }
+    }
 
     return {
       total,
diff --git a/src/features/boulder-state/top-level-task.ts b/src/features/boulder-state/top-level-task.ts
index d92970b56..feff10f0c 100644
--- a/src/features/boulder-state/top-level-task.ts
+++ b/src/features/boulder-state/top-level-task.ts
@@ -6,6 +6,7 @@ const TODO_HEADING_PATTERN = /^##\s+TODOs\b/i
 const FINAL_VERIFICATION_HEADING_PATTERN = /^##\s+Final Verification Wave\b/i
 const SECOND_LEVEL_HEADING_PATTERN = /^##\s+/
 const UNCHECKED_CHECKBOX_PATTERN = /^(\s*)[-*]\s*\[\s*\]\s*(.+)$/
+const CHECKED_CHECKBOX_PATTERN = /^(\s*)[-*]\s*\[[xX]\]\s*(.+)$/
 const TODO_TASK_PATTERN = /^(\d+)\.\s+(.+)$/
 const FINAL_WAVE_TASK_PATTERN = /^(F\d+)\.\s+(.+)$/i