You can copy out the numpy/core/lib/npy-pkg-config directory, add a pkgdir value to the .ini files and set NPY_PKG_CONFIG_PATH environment variable to point to the directory with the modified npy-pkg-config files. Example npymath.ini modified for cross-compilation:: [meta] Name=npymath Description=Portable, core math library implementing C99 standard Version=0.1 [variables] pkgname=numpy.core pkgdir=/build/arm-linux-gnueabi/sysroot/usr/lib/python3.7/site-packages/numpy/core prefix=${pkgdir} libdir=${prefix}/lib includedir=${prefix}/include [default] Libs=-L${libdir} -lnpymath Cflags=-I${includedir} Requires=mlib [msvc] Libs=/LIBPATH:${libdir} npymath.lib Cflags=/INCLUDE:${includedir} Requires=mlib N)