diff --git a/multimedia/mlt/Portfile b/multimedia/mlt/Portfile
index a1808b97fca..140da77daa5 100644
--- a/multimedia/mlt/Portfile
+++ b/multimedia/mlt/Portfile
@@ -86,6 +86,10 @@ depends_lib-append  port:frei0r-plugins \
 configure.pkg_config_path-append \
                     ${prefix}/libexec/ffmpeg${ffmpeg_ver}/lib/pkgconfig
 
+# Don't pick up headers from ffmpeg port if installed, leading to link failure.
+configure.cppflags-replace \
+                    -I${prefix}/include -isystem${prefix}/include
+
 configure.args-append \
                     -DGPL=ON \
                     -DGPL3=OFF \