C++ (or c code for that matter) that needs to link to any libraries will not compile with babel. In the function org-babel-C-execute, the file name is given last, making it impossible to pass compiler flags that will effect linking. A simple fix is to switch the order of the last two arguments to format. Emacs : GNU Emacs 24.3.1 (x86_64-pc-linux-gnu, GTK+ Version 3.10.7) of 2014-03-07 on lamiak, modified by Debian Package: Org-mode version 8.2.10 (8.2.10-29-g89a0ac-elpa @ /home/seth/.emacs.d/elpa/org-20150112/) current state: ============== (setq org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-html-format-drawer-function '(lambda (name contents) contents) org-latex-format-inlinetask-function 'ignore org-confirm-shell-link-function 'yes-or-no-p org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-special-ctrl-a/e t org-latex-format-headline-function 'org-latex-format-headline-default-function org-after-todo-state-change-hook '(org-clock-out-if-current) org-latex-format-drawer-function '(lambda (name contents) contents) org-from-is-user-regexp "\\" org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5] org-babel-result-hide-spec org-babel-hide-all-hashes) org-ascii-format-drawer-function '(lambda (name contents width) contents) org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-babel-tangle-lang-exts '(("C++" . "cpp") ("emacs-lisp" . "el")) org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-html-format-headline-function 'ignore org-babel-load-languages '((gnuplot . t) (emacs-lisp . t) (C . t)) org-html-format-inlinetask-function 'ignore org-clock-out-hook '(org-clock-remove-empty-clock-drawer) org-src-fontify-natively t )