diff --git a/.changeset/rapid-jays-wave.md b/.changeset/rapid-jays-wave.md
new file mode 100644
index 000000000..4a26ec0f2
--- /dev/null
+++ b/.changeset/rapid-jays-wave.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 1663
+---
+**`phase complete` no longer duplicates a By-Phase row when the phase number's padding differs** — completing a phase by its unpadded number (e.g. `phase complete 5`) against an existing zero-padded By-Phase row (`| 05 |`) appended a second `| 5 |` row instead of updating it, double-counting the phase in any column sum. The row matcher now canonicalizes a numeric phase to its integer form (matching `5`, `05`, `005` in either direction), so the existing row is upserted regardless of padding.
diff --git a/src/state.cts b/src/state.cts
index 51def1cf3..f35b56879 100644
--- a/src/state.cts
+++ b/src/state.cts
@@ -2425,7 +2425,12 @@ function updatePerformanceMetricsSection(content: string, cwd: string, phaseNum:
   const byPhaseMatch = content.match(byPhaseTablePattern);
   if (byPhaseMatch) {
     let tableBody = byPhaseMatch[2].trim();
-    const phaseRowPattern = new RegExp(`^\\|\\s*${escapeRegex(String(phaseNum))}\\s*\\|.*$`, 'm');
+    // Match the existing row for this phase, tolerating leading-zero padding in either
+    // direction (#1659): canonicalize a numeric phase to its integer form so a seeded
+    // "| 05 |" row is upserted (not duplicated) by `phase complete 5`, and vice-versa.
+    const phaseNumStr = String(phaseNum);
+    const canonCell = /^\d+$/.test(phaseNumStr) ? `0*${Number(phaseNumStr)}` : escapeRegex(phaseNumStr);
+    const phaseRowPattern = new RegExp(`^\\|\\s*${canonCell}\\s*\\|.*$`, 'm');
     const newRow = `| ${phaseNum} | ${summaryCount} | - | - |`;
 
     if (phaseRowPattern.test(tableBody)) {
diff --git a/tests/state.test.cjs b/tests/state.test.cjs
index 38eb079a8..05ec42f55 100644
--- a/tests/state.test.cjs
+++ b/tests/state.test.cjs
@@ -2267,6 +2267,40 @@ describe('updatePerformanceMetricsSection', () => {
       'velocity total must update from the CRLF STATE.md body (proves CRLF content is processed)',
     );
   });
+
+  test('#1659 — completing an unpadded phase number upserts an existing zero-padded By-Phase row (no duplicate)', () => {
+    const content = [
+      '# Project State', '',
+      '**Current Phase:** 05', '**Status:** Executing Phase 5', '',
+      '## Performance Metrics', '',
+      '**Velocity:**', '- Total plans completed: 1', '- Average duration: N/A', '- Total execution time: 0 hours', '',
+      '**By Phase:**', '',
+      '| Phase | Plans | Total | Avg/Plan |',
+      '|-------|-------|-------|----------|',
+      '| 05 | 1 | - | - |',   // seeded ZERO-PADDED row
+      '',
+      '## Accumulated Context', '',
+    ].join('\n');
+    const statePath = path.join(tmpDir, '.planning', 'STATE.md');
+    fs.writeFileSync(statePath, content, 'utf8');
+
+    const phaseDir = path.join(tmpDir, '.planning', 'phases', '05-final');
+    fs.mkdirSync(phaseDir, { recursive: true });
+    fs.writeFileSync(path.join(phaseDir, '05-01-PLAN.md'), '# Plan\n');
+    fs.writeFileSync(path.join(phaseDir, '05-01-SUMMARY.md'), '# Summary\n');
+    writePassedVerification(tmpDir, '05-final', '05');
+    fs.writeFileSync(path.join(tmpDir, '.planning', 'ROADMAP.md'), '# Roadmap\n\n## Phase 5: Final\n\n- [ ] Phase 5\n');
+
+    // phase complete with the UNPADDED number "5" — must upsert the seeded "| 05 |" row,
+    // not append a duplicate "| 5 |".
+    const result = runGsdTools('phase complete 5', tmpDir);
+    assert.ok(result.success, `phase complete failed: ${result.error}`);
+
+    const after = fs.readFileSync(statePath, 'utf8');
+    const rows05 = (after.match(/^\|\s*05\s*\|/gm) || []).length;
+    const rows5 = (after.match(/^\|\s*5\s*\|/gm) || []).length;
+    assert.equal(rows05 + rows5, 1, `phase 5 must appear exactly once in By Phase (got |05|=${rows05} |5|=${rows5}) — padded/unpadded must dedup (#1659)`);
+  });
 });
 
 // ─────────────────────────────────────────────────────────────────────────────