diff --git a/doxygen/README.md b/doxygen/README.md
index 1a5c41b1aa0..8f38eb9d684 100644
--- a/doxygen/README.md
+++ b/doxygen/README.md
@@ -125,8 +125,7 @@ export TBB_LIB="$TBB/lib/intel64/gcc4.8"
 
 - Set `Stan` local compiler flags to use the new TBB interface:
 ```bash
-mkdir -p ~/.config/stan
-echo TBB_INTERFACE_NEW=true>> ~/.config/stan/make.local
+echo TBB_INTERFACE_NEW=true>> ./make/local
 ```
 
 Compilers
diff --git a/doxygen/contributor_help_pages/developer_doc.md b/doxygen/contributor_help_pages/developer_doc.md
index 687eb1b157d..18dfb1b1fe5 100644
--- a/doxygen/contributor_help_pages/developer_doc.md
+++ b/doxygen/contributor_help_pages/developer_doc.md
@@ -165,9 +165,7 @@ Within the Math library, the only build targets are the tests (there are no othe
 
 ## Makefile Variables
 
-To customize how the tests are built in C++, variables can be set in a file called `make/local`. This is the preferred way of customizing the build. You can also set it more permanently by setting variables in `~/.config/stan/make.local`.
-
-Note: variables in `make/local` override variables in `~/.config/stan/make/local`.
+To customize how the tests are built in C++, variables can be set in a file called `make/local`. This is the preferred way of customizing the build.
 
 There are a lot of make variables that can be set. In general, `CXXFLAGS_*` is for C++ compiler flags, `CPPFLAGS_*` is for C preprocessor flags, `LDFLAGS_*` is for linker flags, and `LDLBIS_*` is for libraries that need to be linked in.
 
@@ -310,7 +308,7 @@ If you want to use custom locations for the library locations, set these makefil
 - `GTEST`
 - `CPPLINT` (optional)
 
-Example `~/.config/stan/make.local` file:
+Example `make/local` file:
 ```
 BOOST = ~/boost
 ```
diff --git a/make/standalone b/make/standalone
index 782f95a9fe3..1dfc9203af1 100644
--- a/make/standalone
+++ b/make/standalone
@@ -14,7 +14,6 @@
 
 MATH_MAKE ?=$(dir $(abspath $(firstword $(MAKEFILE_LIST))))
 MATH ?= $(realpath $(MATH_MAKE)..)/
--include $(HOME)/.config/stan/make.local
 -include $(MATH)make/local
 -include $(MATH)make/compiler_flags
 -include $(MATH)make/libraries
diff --git a/makefile b/makefile
index 3a451ce2635..caa090f56c3 100644
--- a/makefile
+++ b/makefile
@@ -2,16 +2,11 @@
 # Stan Math Library
 # -----------------
 #
-# To customize your build, set make variables in either:
-#    ~/.config/stan/make.local
-#    make/local
-# Variables in make/local is loaded after ~/.config/stan/make.local
-
+# To customize your build, set make variables in the file make/local.
 
 ## 'help' is the default make target.
 help:
 
--include $(HOME)/.config/stan/make.local  # user-defined variables
 -include make/local                       # user-defined variables
 
 include make/compiler_flags               # CXX, CXXFLAGS, LDFLAGS set by the end of this file