diff --git a/.changeset/pretty-dragons-know.md b/.changeset/pretty-dragons-know.md
new file mode 100644
index 000000000..419bd47a2
--- /dev/null
+++ b/.changeset/pretty-dragons-know.md
@@ -0,0 +1,5 @@
+---
+'skuba': patch
+---
+
+**configure:** Reserve skuba-managed sections in ignore files
diff --git a/src/cli/configure/analysis/__snapshots__/project.test.ts.snap b/src/cli/configure/analysis/__snapshots__/project.test.ts.snap
index d4954d7b9..20675e8ef 100644
--- a/src/cli/configure/analysis/__snapshots__/project.test.ts.snap
+++ b/src/cli/configure/analysis/__snapshots__/project.test.ts.snap
@@ -3,7 +3,8 @@
 exports[`diffFiles works from scratch 1`] = `
 Object {
   ".dockerignore": Object {
-    "data": ".idea/
+    "data": "# managed by skuba
+.idea/
 .serverless/
 .vscode/
 node_modules*/
@@ -17,11 +18,13 @@ node_modules*/
 .npmrc
 npm-debug.log
 yarn-error.log
+# end managed by skuba
 ",
     "operation": "A",
   },
   ".eslintignore": Object {
-    "data": ".idea/
+    "data": "# managed by skuba
+.idea/
 .serverless/
 .vscode/
 node_modules*/
@@ -30,6 +33,7 @@ node_modules*/
 /dist*/
 /lib*/
 /tmp*/
+# end managed by skuba
 ",
     "operation": "A",
   },
@@ -48,7 +52,8 @@ node_modules*/
     "operation": "A",
   },
   ".gitignore": Object {
-    "data": ".idea/
+    "data": "# managed by skuba
+.idea/
 .serverless/
 .vscode/
 node_modules*/
@@ -64,11 +69,13 @@ node_modules*/
 npm-debug.log
 package-lock.json
 yarn-error.log
+# end managed by skuba
 ",
     "operation": "A",
   },
   ".prettierignore": Object {
-    "data": ".idea/
+    "data": "# managed by skuba
+.idea/
 .serverless/
 .vscode/
 node_modules*/
@@ -81,6 +88,7 @@ node_modules*/
 # Gantry resource files support non-standard template syntax
 gantry*.yaml
 gantry*.yml
+# end managed by skuba
 ",
     "operation": "A",
   },
diff --git a/src/cli/configure/processing/__snapshots__/ignoreFile.test.ts.snap b/src/cli/configure/processing/__snapshots__/ignoreFile.test.ts.snap
index 3dd466b4d..e0a1a4a86 100644
--- a/src/cli/configure/processing/__snapshots__/ignoreFile.test.ts.snap
+++ b/src/cli/configure/processing/__snapshots__/ignoreFile.test.ts.snap
@@ -1,44 +1,58 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`mergeWithIgnoreFile difference 1`] = `
-"node_modules
-
-.DS_Store
+exports[`mergeWithIgnoreFile empty provided 1`] = `
+"# managed by skuba
+node_modules
+# end managed by skuba
 "
 `;
 
-exports[`mergeWithIgnoreFile empty 1`] = `
-"
-"
+exports[`mergeWithIgnoreFile identical 1`] = `
+"# managed by skuba
+node_modules
+# end managed by skuba"
 `;
 
-exports[`mergeWithIgnoreFile empty base 1`] = `
-"node_modules
-"
-`;
+exports[`mergeWithIgnoreFile provided with managed section and additional lines 1`] = `
+".idea
+.vscode
 
-exports[`mergeWithIgnoreFile empty provided 1`] = `
-"node_modules
-"
-`;
+# managed by skuba
+node_modules
+# end managed by skuba
 
-exports[`mergeWithIgnoreFile identical 1`] = `
-"node_modules
+.DS_Store
+node_modules
 "
 `;
 
-exports[`mergeWithIgnoreFile mix 1`] = `
-".DS_Store
+exports[`mergeWithIgnoreFile provided with no managed section 1`] = `
+"# managed by skuba
+node_modules
+# end managed by skuba
 
-yarn-error.log
+.DS_Store
+"
+`;
 
+exports[`mergeWithIgnoreFile provided with outdated managed section 1`] = `
+"# managed by skuba
 node_modules
+.DS_Store
+# end managed by skuba
 "
 `;
 
-exports[`mergeWithIgnoreFile whitespace 1`] = `
-"node_modules
+exports[`mergeWithIgnoreFile provided with outdated managed section and additional lines 1`] = `
+".idea
+.vscode
+
+# managed by skuba
+node_modules
+.DS_Store
+# end managed by skuba
 
 .DS_Store
+node_modules
 "
 `;
diff --git a/src/cli/configure/processing/ignoreFile.test.ts b/src/cli/configure/processing/ignoreFile.test.ts
index b0c1bf9e4..2b3be3778 100644
--- a/src/cli/configure/processing/ignoreFile.test.ts
+++ b/src/cli/configure/processing/ignoreFile.test.ts
@@ -1,17 +1,30 @@
 import { mergeWithIgnoreFile } from './ignoreFile';
 
 describe('mergeWithIgnoreFile', () => {
+  const baseTemplate =
+    '# managed by skuba\nnode_modules\n# end managed by skuba';
+  const updatedBaseTemplate =
+    '# managed by skuba\nnode_modules\n.DS_Store\n# end managed by skuba';
+
   const cases = [
-    ['difference', 'node_modules', '.DS_Store'],
-    ['empty', '', ''],
-    ['empty base', '', 'node_modules'],
-    ['empty provided', 'node_modules', ''],
-    ['identical', 'node_modules', 'node_modules'],
-    ['mix', '.DS_Store\n\nyarn-error.log', '\n\n.DS_Store\n\nnode_modules'],
+    ['empty provided', baseTemplate, ''],
+
+    ['provided with no managed section', baseTemplate, '.DS_Store\n'],
+    [
+      'provided with outdated managed section',
+      updatedBaseTemplate,
+      `${baseTemplate}\n`,
+    ],
+    ['identical', baseTemplate, baseTemplate],
+    [
+      'provided with managed section and additional lines',
+      baseTemplate,
+      `.idea\n.vscode\n\n${baseTemplate}\n\n.DS_Store\nnode_modules\n`,
+    ],
     [
-      'whitespace',
-      '\n   \n  node_modules  \n\n \n  ',
-      '\n  \n   .DS_Store\n\n  ',
+      'provided with outdated managed section and additional lines',
+      updatedBaseTemplate,
+      `.idea\n.vscode\n\n${baseTemplate}\n\n.DS_Store\nnode_modules\n`,
     ],
   ] as const;
 
diff --git a/src/cli/configure/processing/ignoreFile.ts b/src/cli/configure/processing/ignoreFile.ts
index 67b76335c..49b8c3cf3 100644
--- a/src/cli/configure/processing/ignoreFile.ts
+++ b/src/cli/configure/processing/ignoreFile.ts
@@ -1,25 +1,20 @@
-const splitIntoSanitisedLines = (str: string) =>
-  str
-    .trim()
-    .split(/\r?\n/)
-    .map((line) => line.trim());
-
 export const mergeWithIgnoreFile = (templateFile: string) => (
   inputFile?: string,
 ) => {
-  const templateLines = splitIntoSanitisedLines(templateFile);
-
-  const templateSet = new Set(templateLines.filter((line) => line !== ''));
+  if (typeof inputFile === 'undefined') {
+    return templateFile;
+  }
 
-  const inputLines = splitIntoSanitisedLines(inputFile ?? '').filter(
-    (line) => !templateSet.has(line),
+  const replacedFile = inputFile.replace(
+    /# managed by skuba[\s\S]*# end managed by skuba/,
+    templateFile,
   );
 
-  const outputFile = [
-    templateLines.join('\n').trim(),
-    inputLines.join('\n').trim(),
-  ]
-    .filter((blob) => blob !== '')
+  if (replacedFile.includes(templateFile)) {
+    return replacedFile;
+  }
+
+  const outputFile = [templateFile.trim(), inputFile.trim()]
     .join('\n\n')
     .trim();
 
diff --git a/template/base/_.dockerignore b/template/base/_.dockerignore
index bc56d0a6e..c2aa9db21 100644
--- a/template/base/_.dockerignore
+++ b/template/base/_.dockerignore
@@ -1,3 +1,4 @@
+# managed by skuba
 .idea/
 .serverless/
 .vscode/
@@ -12,3 +13,4 @@ node_modules*/
 .npmrc
 npm-debug.log
 yarn-error.log
+# end managed by skuba
diff --git a/template/base/_.eslintignore b/template/base/_.eslintignore
index 21fca81d3..a32542c71 100644
--- a/template/base/_.eslintignore
+++ b/template/base/_.eslintignore
@@ -1,3 +1,4 @@
+# managed by skuba
 .idea/
 .serverless/
 .vscode/
@@ -7,3 +8,4 @@ node_modules*/
 /dist*/
 /lib*/
 /tmp*/
+# end managed by skuba
diff --git a/template/base/_.gitignore b/template/base/_.gitignore
index 54e802c71..0bb0933d6 100644
--- a/template/base/_.gitignore
+++ b/template/base/_.gitignore
@@ -1,3 +1,4 @@
+# managed by skuba
 .idea/
 .serverless/
 .vscode/
@@ -14,3 +15,4 @@ node_modules*/
 npm-debug.log
 package-lock.json
 yarn-error.log
+# end managed by skuba
diff --git a/template/base/_.prettierignore b/template/base/_.prettierignore
index 44890f1e7..f1256f149 100644
--- a/template/base/_.prettierignore
+++ b/template/base/_.prettierignore
@@ -1,3 +1,4 @@
+# managed by skuba
 .idea/
 .serverless/
 .vscode/
@@ -11,3 +12,4 @@ node_modules*/
 # Gantry resource files support non-standard template syntax
 gantry*.yaml
 gantry*.yml
+# end managed by skuba