I have successfully done this by doing the following: 1. export CC, CXX etc (to be location of custom gcc) 2. edit user-config.jam (specifying location of custom gcc) 3. run bootstrap 4. run b2 (specifying toolset=gcc) Please excuse the variables I have in the following examples but I've taken this from some scripts we have for our own in-house sdk. I think you should be able to get the gist: export AR="${GCC_LOC}/ar" export CC="${GCC_LOC}/gcc" export CPP="${GCC_LOC}/gcc -E" export CXX="${GCC_LOC}/g++" export CXXCPP="${GCC_LOC}/g++ -E" pushd boost_${BOOST_DL_VERSION} > /dev/null # add our compiler to the end of the boost jam config file cat <<EOF > ./tools/build/v2/user-config.jam using gcc : : ${GCC_LOC}/g++ ; EOF BOOST_LIBRARIES=filesystem,python,regex,system CONFIGURE_OPTIONS="--with-python-version=2.7 --with-python-root=${PYTHON_LOC}/${OS}/${ARCH} --with-python=${PYTHON_LOC}/${OS}/${ARCH}/bin/python" ./bootstrap.sh --prefix=${PREFIX} --with-libraries=${BOOST_LIBRARIES} ${CONFIGURE_OPTIONS} ./b2 $CPPFLAGS --toolset=gcc