diff --git a/.changeset/fuzzy-pots-think.md b/.changeset/fuzzy-pots-think.md
new file mode 100644
index 000000000..39a82b319
--- /dev/null
+++ b/.changeset/fuzzy-pots-think.md
@@ -0,0 +1,6 @@
+---
+"markdown-it-myst": patch
+"myst-parser": patch
+---
+
+Only trim end of line for myst-directives, not both the start and end of lines. This is important for keeping indentation in code blocks.
diff --git a/packages/markdown-it-myst/src/directives.ts b/packages/markdown-it-myst/src/directives.ts
index cdc07435e..dc36073ca 100644
--- a/packages/markdown-it-myst/src/directives.ts
+++ b/packages/markdown-it-myst/src/directives.ts
@@ -56,7 +56,7 @@ function runDirectives(state: StateCore): boolean {
           body.shift();
           bodyOffset++;
         }
-        const bodyString = body.join('\n').trim();
+        const bodyString = body.join('\n').trimEnd();
         const directiveOpen = new state.Token('parsed_directive_open', '', 1);
         directiveOpen.info = info;
         directiveOpen.hidden = true;
diff --git a/packages/myst-parser/tests/directives/code.yml b/packages/myst-parser/tests/directives/code.yml
index 76e733194..355eb3572 100644
--- a/packages/myst-parser/tests/directives/code.yml
+++ b/packages/myst-parser/tests/directives/code.yml
@@ -24,6 +24,34 @@ cases:
               value: |-
                 # here is math
                 1+2
+  - title: code-block with indentation
+    markdown: |-
+      ```{code-block} c
+      :linenos: true
+      :lineno-start: 2
+      :emphasize-lines: 3
+          for (int i = 0; i < 10; i++) {
+              /* do something */
+          }
+      ```
+    mdast:
+      type: root
+      children:
+        - type: mystDirective
+          name: code-block
+          args: c
+          options:
+            emphasize-lines: 3
+            lineno-start: 2
+            linenos: true
+          value: "    for (int i = 0; i < 10; i++) {\n        /* do something */\n    }"
+          children:
+            - type: code
+              lang: c
+              showLineNumbers: true
+              startingLineNumber: 2
+              emphasizeLines: [3]
+              value: "    for (int i = 0; i < 10; i++) {\n        /* do something */\n    }"
   - title: code-block with name language options parses
     markdown: |-
       ```{code-block} python
diff --git a/packages/myst-parser/tests/myst.spec.ts b/packages/myst-parser/tests/myst.spec.ts
index b23069ac0..00169acfb 100644
--- a/packages/myst-parser/tests/myst.spec.ts
+++ b/packages/myst-parser/tests/myst.spec.ts
@@ -85,8 +85,10 @@ function stripPositions(tree: GenericParent) {
   return tree;
 }
 
-function removeTightAnnotations(tree: GenericParent) {
+function fixMystDirectives(tree: GenericParent) {
   selectAll('mystDirective', tree).forEach((node) => {
+    // Node markdown is trimmed
+    (node as any).value = (node as any).value?.trim();
     // These are added on afterwards and we aren't taking them into account in myst spec
     delete (node as any).tight;
   });
@@ -115,7 +117,7 @@ describe('Testing myst --> mdast conversions', () => {
   test.each(mystCases)('%s', (_, { myst, mdast }) => {
     if (myst) {
       const mdastString = yaml.dump(mdast);
-      const newAst = removeTightAnnotations(
+      const newAst = fixMystDirectives(
         replaceMystCommentNodes(
           stripPositions(
             mystParse(myst, {