You seem to be invoking the compiler separately for the sole purpose of building .d files (with a %.d: %.c rule). Don't do it that way. With the -MMD option, yo

You seem to be invoking the compiler separately for the sole purpose of building .d files (with a %.d: %.c rule). Don't do it that way. With the -MMD option, you create the .d file as a side-effect of the real compilation. Any change that would require the .d file to be rebuilt has to involve a change to the old dependencies as listed in the old .d file. So the source file will be recompiled. In order for a new dependency on a new header file to be added, an existing and remaining dependency needs to change to add '#include ...'. So the .c file will get recompiled because that file has changed and then you have a new .d file. For C/C++, I have to subvert GNU make's attempts to rebuild .d files by using $(wildcard) on them and inserting a /./ in the middle of the path. Note that there are other cases where I do have a rule for building .d files and have them rebuilt. In particular for Fortran 90 modules. This occurs wherever you need to build the .d files first for the initial first build to be in the correct order. This is only an issue for C/C++ if you are invoking a program to generate C sources (e.g. rpcgen). In practice, that is often best handled with a few dependencies listed explicitly in your Makefile.