diff --git a/R/use_extendr.R b/R/use_extendr.R
index 7c62d9c7..a878c49c 100644
--- a/R/use_extendr.R
+++ b/R/use_extendr.R
@@ -101,16 +101,16 @@ use_extendr <- function(path = ".",
   )
 
   use_rextendr_template(
-    "Makevars",
-    save_as = file.path("src", "Makevars"),
+    "Makevars.in",
+    save_as = file.path("src", "Makevars.in"),
     quiet = quiet,
     overwrite = overwrite,
     data = list(lib_name = lib_name)
   )
 
   use_rextendr_template(
-    "Makevars.win",
-    save_as = file.path("src", "Makevars.win"),
+    "Makevars.win.in",
+    save_as = file.path("src", "Makevars.win.in"),
     quiet = quiet,
     overwrite = overwrite,
     data = list(lib_name = lib_name)
@@ -179,7 +179,7 @@ use_extendr <- function(path = ".",
 
   # add msrv.R template
   use_rextendr_template(
-    "cran/msrv.R",
+    "msrv.R",
     save_as = file.path("tools", "msrv.R"),
     quiet = quiet,
     overwrite = overwrite
@@ -187,27 +187,35 @@ use_extendr <- function(path = ".",
 
   # add configure and configure.win templates
   use_rextendr_template(
-    "cran/configure",
+    "configure",
     save_as = "configure",
     quiet = quiet,
     overwrite = overwrite,
     data = list(lib_name = lib_name)
   )
 
-  # configure needs to be made executable
-  # ignore for Windows
-  if (.Platform[["OS.type"]] == "unix") {
-    Sys.chmod("configure", "0755")
-  }
+  use_rextendr_template(
+    "cleanup",
+    save_as = "cleanup",
+    quiet = quiet,
+    overwrite = overwrite,
+    data = list(lib_name = lib_name)
+  )
 
   use_rextendr_template(
-    "cran/configure.win",
+    "configure.win",
     save_as = "configure.win",
     quiet = quiet,
     overwrite = overwrite,
     data = list(lib_name = lib_name)
   )
 
+  # configure needs to be made executable
+  # ignore for Windows
+  if (.Platform[["OS.type"]] == "unix") {
+    Sys.chmod("configure", "0755")
+    Sys.chmod("cleanup", "0755")
+  }
 
   if (!isTRUE(quiet)) {
     cli::cli_alert_success("Finished configuring {.pkg extendr} for package {.pkg {pkg_name}}.")
diff --git a/inst/templates/Makevars b/inst/templates/Makevars
deleted file mode 100644
index eba6dd7f..00000000
--- a/inst/templates/Makevars
+++ /dev/null
@@ -1,33 +0,0 @@
-TARGET_DIR = ./rust/target
-LIBDIR = $(TARGET_DIR)/release
-STATLIB = $(LIBDIR)/lib{{{lib_name}}}.a
-PKG_LIBS = -L$(LIBDIR) -l{{{lib_name}}}
-
-# Print linked static libraries at compile time
-export RUSTFLAGS += --print=native-static-libs
-
-all: C_clean
-
-$(SHLIB): $(STATLIB)
-
-CARGOTMP = $(CURDIR)/.cargo
-
-$(STATLIB):
-	# In some environments, ~/.cargo/bin might not be included in PATH, so we need
-	# to set it here to ensure cargo can be invoked. It is appended to PATH and
-	# therefore is only used if cargo is absent from the user's PATH.
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		export CARGO_HOME=$(CARGOTMP); \
-	fi && \
-		export PATH="$(PATH):$(HOME)/.cargo/bin" && \
-		cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		rm -Rf $(CARGOTMP) && \
-		rm -Rf $(LIBDIR)/build; \
-	fi
-
-C_clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
-
-clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR)
diff --git a/inst/templates/Makevars.in b/inst/templates/Makevars.in
new file mode 100644
index 00000000..19d72678
--- /dev/null
+++ b/inst/templates/Makevars.in
@@ -0,0 +1,50 @@
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/release
+STATLIB = $(LIBDIR)/lib{{{lib_name}}}.a
+PKG_LIBS = -L$(LIBDIR) -l{{{lib_name}}}
+
+all: C_clean
+
+$(SHLIB): $(STATLIB)
+
+CARGOTMP = $(CURDIR)/.cargo
+VENDOR_DIR = $(CURDIR)/vendor
+
+
+# RUSTFLAGS appends --print=native-static-libs to ensure that 
+# the correct linkers are used. Use this for debugging if need. 
+#
+# CRAN note: Cargo and Rustc versions are reported during
+# configure via tools/msrv.R.
+#
+# When on CRAN, the vendor.tar.xz file is unzipped and used
+# for offline compilation. It is ignored when NOT_CRAN != false
+$(STATLIB):
+
+	# Check if NOT_CRAN is false and unzip vendor.tar.xz if so
+	if [ "$(NOT_CRAN)" = "false" ]; then \
+		if [ -f ./rust/vendor.tar.xz ]; then \
+			tar xf rust/vendor.tar.xz && \
+			mkdir -p $(CARGOTMP) && \
+			cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
+		fi; \
+	fi
+
+	export CARGO_HOME=$(CARGOTMP) && \
+	export PATH="$(PATH):$(HOME)/.cargo/bin" && \
+	RUSTFLAGS="$(RUSTFLAGS) --print=native-static-libs" cargo build @CRAN_FLAGS@ --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
+
+	# Always clean up CARGOTMP
+	rm -Rf $(CARGOTMP)
+
+ 	if [ "$(NOT_CRAN)" != "false" ]; then \
+        rm -Rf $(VENDOR_DIR); \
+        rm -Rf $(TARGET_DIR); \
+        rm -Rf $(LIBDIR)/build; \
+    fi
+
+C_clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR) $(VENDOR_DIR)
diff --git a/inst/templates/Makevars.win b/inst/templates/Makevars.win.in
similarity index 53%
rename from inst/templates/Makevars.win
rename to inst/templates/Makevars.win.in
index 9bdff35c..ae47cd81 100644
--- a/inst/templates/Makevars.win
+++ b/inst/templates/Makevars.win.in
@@ -5,9 +5,6 @@ LIBDIR = $(TARGET_DIR)/$(TARGET)/release
 STATLIB = $(LIBDIR)/lib{{{lib_name}}}.a
 PKG_LIBS = -L$(LIBDIR) -l{{{lib_name}}} -lws2_32 -ladvapi32 -luserenv -lbcrypt -lntdll
 
-# Print linked static libraries at compile time
-export RUSTFLAGS += --print=native-static-libs
-
 all: C_clean
 
 $(SHLIB): $(STATLIB)
@@ -24,18 +21,30 @@ $(STATLIB):
 	# https://github.com/r-windows/rtools-packages/blob/2407b23f1e0925bbb20a4162c963600105236318/mingw-w64-gcc/PKGBUILD#L313-L316
 	touch $(TARGET_DIR)/libgcc_mock/libgcc_eh.a
 
-	# CARGO_LINKER is provided in Makevars.ucrt for R >= 4.2
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		export CARGO_HOME=$(CARGOTMP); \
-	fi && \
-		export CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER="$(CARGO_LINKER)" && \
-		export LIBRARY_PATH="$${LIBRARY_PATH};$(CURDIR)/$(TARGET_DIR)/libgcc_mock" && \
-		cargo build --target=$(TARGET) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		rm -Rf $(CARGOTMP) && \
-		rm -Rf $(LIBDIR)/build; \
+	# Handle NOT_CRAN case: If NOT_CRAN is false, vendor tarball should be handled
+	if [ "$(NOT_CRAN)" = "false" ]; then \
+		if [ -f ./rust/vendor.tar.xz ]; then \
+			tar xf rust/vendor.tar.xz && \
+			mkdir -p $(CARGOTMP) && \
+			cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
+		fi; \
 	fi
 
+	# Build the project using Cargo with additional flags
+	export CARGO_HOME=$(CARGOTMP) && \
+	export CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER="$(CARGO_LINKER)" && \
+	export LIBRARY_PATH="$${LIBRARY_PATH};$(CURDIR)/$(TARGET_DIR)/libgcc_mock" && \
+	RUSTFLAGS="$(RUSTFLAGS) --print=native-static-libs" cargo @CRAN_FLAGS@ build --target=$(TARGET) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
+
+	# Always clean up CARGOTMP
+	rm -Rf $(CARGOTMP)
+
+ 	if [ "$(NOT_CRAN)" != "false" ]; then \
+        rm -Rf $(VENDOR_DIR); \
+        rm -Rf $(TARGET_DIR); \
+        rm -Rf $(LIBDIR)/build; \
+    fi
+
 C_clean:
 	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
 
diff --git a/inst/templates/cleanup b/inst/templates/cleanup
new file mode 100644
index 00000000..ec35c3f8
--- /dev/null
+++ b/inst/templates/cleanup
@@ -0,0 +1,4 @@
+# removes the Makevars file generated by configure
+# this allows the Makevars file to be generated each
+# time the build is called
+rm -rf src/Makevars
\ No newline at end of file
diff --git a/inst/templates/configure b/inst/templates/configure
new file mode 100644
index 00000000..3aab1212
--- /dev/null
+++ b/inst/templates/configure
@@ -0,0 +1,13 @@
+#!/usr/bin/env sh
+: "${R_HOME=`R RHOME`}"
+"${R_HOME}/bin/Rscript" tools/msrv.R 
+
+# Set CRAN_FLAGS based on the NOT_CRAN value
+if [ "${NOT_CRAN}" = "false" ]; then
+  export CRAN_FLAGS="-j 2 --offline"
+else
+  export CRAN_FLAGS=""
+fi
+
+# Substitute @CRAN_FLAGS@ in Makevars.in with the actual value of $CRAN_FLAGS
+sed -e "s|@CRAN_FLAGS@|$CRAN_FLAGS|" src/Makevars.in > src/Makevars
\ No newline at end of file
diff --git a/inst/templates/configure.win b/inst/templates/configure.win
new file mode 100644
index 00000000..40335385
--- /dev/null
+++ b/inst/templates/configure.win
@@ -0,0 +1,12 @@
+#!/usr/bin/env sh
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/msrv.R
+
+# Set CRAN_FLAGS based on the NOT_CRAN value
+if [ "${NOT_CRAN}" = "false" ]; then
+  export CRAN_FLAGS="-j 2 --offline"
+else
+  export CRAN_FLAGS=""
+fi
+
+# Substitute @CRAN_FLAGS@ in Makevars.in with the actual value of $CRAN_FLAGS
+sed -e "s|@CRAN_FLAGS@|$CRAN_FLAGS|" src/Makevars.in > src/Makevars
\ No newline at end of file
diff --git a/inst/templates/cran/Makevars b/inst/templates/cran/Makevars
deleted file mode 100644
index 3858063a..00000000
--- a/inst/templates/cran/Makevars
+++ /dev/null
@@ -1,39 +0,0 @@
-TARGET_DIR = ./rust/target
-LIBDIR = $(TARGET_DIR)/release
-STATLIB = $(LIBDIR)/lib{{{lib_name}}}.a
-PKG_LIBS = -L$(LIBDIR) -l{{{lib_name}}}
-
-# Print linked static libraries at compile time
-export RUSTFLAGS += --print=native-static-libs
-
-all: C_clean
-
-$(SHLIB): $(STATLIB)
-
-CRAN_FLAGS=-j 2 --offline
-CARGOTMP = $(CURDIR)/.cargo
-VENDOR_DIR = $(CURDIR)/vendor
-
-$(STATLIB):
-	if [ -f ./rust/vendor.tar.xz ]; then \
-		tar xf rust/vendor.tar.xz && \
-		mkdir -p $(CARGOTMP) && \
-		cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
-	fi
-
-	# In some environments, ~/.cargo/bin might not be included in PATH, so we need
-	# to set it here to ensure cargo can be invoked. It is appended to PATH and
-	# therefore is only used if cargo is absent from the user's PATH.
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		export CARGO_HOME=$(CARGOTMP); \
-	fi && \
-		export PATH="$(PATH):$(HOME)/.cargo/bin" && \
-			cargo build $(CRAN_FLAGS) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) && \
-			echo `cargo --version` && echo `rustc --version`;
-		rm -Rf $(CARGOTMP) $(VENDOR_DIR) $(LIBDIR)/build; \
-
-C_clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(CARGOTMP) $(VENDOR_DIR)
-
-clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(CARGOTMP) $(VENDOR_DIR) $(TARGET_DIR)
diff --git a/inst/templates/cran/Makevars.win b/inst/templates/cran/Makevars.win
deleted file mode 100644
index 599ab819..00000000
--- a/inst/templates/cran/Makevars.win
+++ /dev/null
@@ -1,51 +0,0 @@
-TARGET = $(subst 64,x86_64,$(subst 32,i686,$(WIN)))-pc-windows-gnu
-
-TARGET_DIR = ./rust/target
-LIBDIR = $(TARGET_DIR)/$(TARGET)/release
-STATLIB = $(LIBDIR)/lib{{{lib_name}}}.a
-PKG_LIBS = -L$(LIBDIR) -l{{{lib_name}}} -lws2_32 -ladvapi32 -luserenv -lbcrypt -lntdll
-
-# Print linked static libraries at compile time
-export RUSTFLAGS += --print=native-static-libs
-
-all: C_clean
-
-$(SHLIB): $(STATLIB)
-
-CRAN_FLAGS=-j 2 --offline
-CARGOTMP = $(CURDIR)/.cargo
-VENDOR_DIR = $(CURDIR)/vendor
-
-$(STATLIB):
-	# uncompress vendored deps
-	if [ -f ./rust/vendor.tar.xz ]; then \
-		tar xf rust/vendor.tar.xz && \
-		mkdir -p $(CARGOTMP) && \
-		cp rust/vendor-config.toml $(CARGOTMP)/config.toml; \
-	fi
-
-	mkdir -p $(TARGET_DIR)/libgcc_mock
-	# `rustc` adds `-lgcc_eh` flags to the compiler, but Rtools' GCC doesn't have
-	# `libgcc_eh` due to the compilation settings. So, in order to please the
-	# compiler, we need to add empty `libgcc_eh` to the library search paths.
-	# For more details, please refer to
-	# https://github.com/r-windows/rtools-packages/blob/2407b23f1e0925bbb20a4162c963600105236318/mingw-w64-gcc/PKGBUILD#L313-L316
-	touch $(TARGET_DIR)/libgcc_mock/libgcc_eh.a
-
-	# CARGO_LINKER is provided in Makevars.ucrt for R >= 4.2
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		export CARGO_HOME=$(CARGOTMP); \
-	fi && \
-		export CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER="$(CARGO_LINKER)" && \
-		export LIBRARY_PATH="$${LIBRARY_PATH};$(CURDIR)/$(TARGET_DIR)/libgcc_mock"; \
-		cargo build $(CRAN_FLAGS) --target=$(TARGET) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR) && \
-		echo `cargo --version` && echo `rustc --version`;
-	if [ "$(NOT_CRAN)" != "true" ]; then \
-		rm -Rf $(CARGOTMP) $(VENDOR_DIR) $(LIBDIR)/build; \
-	fi
-
-C_clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(CARGOTMP) $(VENDOR_DIR)
-
-clean:
-	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(CARGOTMP) $(VENDOR_DIR) $(TARGET_DIR)
diff --git a/inst/templates/cran/configure b/inst/templates/cran/configure
deleted file mode 100644
index 0f4c1be0..00000000
--- a/inst/templates/cran/configure
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env sh
-: "${R_HOME=`R RHOME`}"
-"${R_HOME}/bin/Rscript" tools/msrv.R 
diff --git a/inst/templates/cran/configure.win b/inst/templates/cran/configure.win
deleted file mode 100644
index f1945ac1..00000000
--- a/inst/templates/cran/configure.win
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/env sh
-"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/msrv.R
diff --git a/inst/templates/cran/msrv.R b/inst/templates/msrv.R
similarity index 100%
rename from inst/templates/cran/msrv.R
rename to inst/templates/msrv.R