diff --git a/src/view/treeNodes/directoryTreeNode.ts b/src/view/treeNodes/directoryTreeNode.ts
index 97098a15ca..b24e8e9b75 100644
--- a/src/view/treeNodes/directoryTreeNode.ts
+++ b/src/view/treeNodes/directoryTreeNode.ts
@@ -124,7 +124,7 @@ export class DirectoryTreeNode extends TreeNode implements vscode.TreeItem {
 				if (!child.allChildrenViewed()) {
 					return false;
 				}
-			} else if (child.checkboxState.state !== vscode.TreeItemCheckboxState.Checked) {
+			} else if (!child.checkboxState || child.checkboxState.state !== vscode.TreeItemCheckboxState.Checked) {
 				return false;
 			}
 		}
diff --git a/src/view/treeNodes/fileChangeNode.ts b/src/view/treeNodes/fileChangeNode.ts
index 350471690b..0b457fdb12 100644
--- a/src/view/treeNodes/fileChangeNode.ts
+++ b/src/view/treeNodes/fileChangeNode.ts
@@ -75,7 +75,7 @@ export class FileChangeNode extends TreeNode implements vscode.TreeItem {
 	public command: vscode.Command;
 	public opts: vscode.TextDocumentShowOptions;
 
-	public checkboxState: { state: vscode.TreeItemCheckboxState; tooltip?: string; accessibilityInformation: vscode.AccessibilityInformation };
+	public checkboxState?: { state: vscode.TreeItemCheckboxState; tooltip?: string; accessibilityInformation: vscode.AccessibilityInformation };
 
 	get status(): GitChangeType {
 		return this.changeModel.status;
@@ -155,13 +155,28 @@ export class FileChangeNode extends TreeNode implements vscode.TreeItem {
 		}
 	}
 
+	/**
+	 * Check if this file node is under a commit node in the tree hierarchy.
+	 * Files under commit nodes should not have checkboxes.
+	 */
+	private isUnderCommitNode(): boolean {
+		// If the file's sha is different from the PR's head sha, it's from an older commit
+		// and should not have a checkbox
+		return this.changeModel.sha !== undefined && this.changeModel.sha !== this.pullRequest.head?.sha;
+	}
+
 	updateViewed(viewed: ViewedState) {
 		this.changeModel.updateViewed(viewed);
 		this.contextValue = `${Schemes.FileChange}:${GitChangeType[this.changeModel.status]}:${viewed === ViewedState.VIEWED ? 'viewed' : 'unviewed'
 			}`;
-		this.checkboxState = viewed === ViewedState.VIEWED ?
-			{ state: vscode.TreeItemCheckboxState.Checked, tooltip: vscode.l10n.t('Mark File as Unviewed'), accessibilityInformation: { label: vscode.l10n.t('Mark file {0} as unviewed', this.label ?? '') } } :
-			{ state: vscode.TreeItemCheckboxState.Unchecked, tooltip: vscode.l10n.t('Mark File as Viewed'), accessibilityInformation: { label: vscode.l10n.t('Mark file {0} as viewed', this.label ?? '') } };
+		// Don't show checkboxes for files under commit nodes
+		if (!this.isUnderCommitNode()) {
+			this.checkboxState = viewed === ViewedState.VIEWED ?
+				{ state: vscode.TreeItemCheckboxState.Checked, tooltip: vscode.l10n.t('Mark File as Unviewed'), accessibilityInformation: { label: vscode.l10n.t('Mark file {0} as unviewed', this.label ?? '') } } :
+				{ state: vscode.TreeItemCheckboxState.Unchecked, tooltip: vscode.l10n.t('Mark File as Viewed'), accessibilityInformation: { label: vscode.l10n.t('Mark file {0} as viewed', this.label ?? '') } };
+		} else {
+			this.checkboxState = undefined;
+		}
 		this.pullRequestManager.setFileViewedContext();
 	}
 
diff --git a/src/view/treeNodes/treeUtils.ts b/src/view/treeNodes/treeUtils.ts
index 3bde5a5863..94920c8718 100644
--- a/src/view/treeNodes/treeUtils.ts
+++ b/src/view/treeNodes/treeUtils.ts
@@ -35,9 +35,10 @@ export namespace TreeUtils {
 					continue;
 				}
 				if (!checkedNodes.includes(selected) && !uncheckedNodes.includes(selected)) {
-					if (selected.checkboxState.state === vscode.TreeItemCheckboxState.Unchecked) {
+					// Only process files that have checkboxes (files without checkboxState, like those under commits, are skipped)
+					if (selected.checkboxState?.state === vscode.TreeItemCheckboxState.Unchecked) {
 						checkedNodes.push(selected);
-					} else {
+					} else if (selected.checkboxState?.state === vscode.TreeItemCheckboxState.Checked) {
 						uncheckedNodes.push(selected);
 					}
 				}