diff --git a/docs/setup.rst b/docs/setup.rst
index 55746b776..65700f241 100644
--- a/docs/setup.rst
+++ b/docs/setup.rst
@@ -37,7 +37,9 @@ Assuming one has ``conda`` in their path, then do the following::
   conda activate fre-cli
 
   # add mkmf to your PATH
-  export PATH=$PATH:${PWD}/mkmf/bin
+  # mkmf PR 75 moved executables from bin/ to mkmf/bin/ within the mkmf repo;
+  # both paths are added here for backwards-compatibility with either version.
+  export PATH=$PATH:${PWD}/fre/mkmf/bin:${PWD}/fre/mkmf/mkmf/bin
 
   # now we pip install the local code under the `fre/` directory
   # the -e flag makes re-installing the code after editing not necessary
diff --git a/fre/make/gfdlfremake/buildDocker.py b/fre/make/gfdlfremake/buildDocker.py
index 87fbf1cfa..2d4cfc0ee 100644
--- a/fre/make/gfdlfremake/buildDocker.py
+++ b/fre/make/gfdlfremake/buildDocker.py
@@ -48,9 +48,11 @@ def __init__(self,base,exp,libs,RUNenv,target,mkTemplate,stage2base):
                 self.setup.append(" && spack load "+l+" \\ \n")
 
         # Clone and copy mkmf through Dockerfile
+        # Backwards-compatible with both old mkmf (bin/) and mkmf PR 75 (mkmf/bin/)
         self.mkmfclone=["RUN cd /apps \\ \n",
                        " && git clone --recursive https://github.com/NOAA-GFDL/mkmf \\ \n",
-                       " && cp mkmf/bin/* /usr/local/bin \n"]
+                       " && if [ -d mkmf/mkmf/bin ]; then cp mkmf/mkmf/bin/* /usr/local/bin;"
+                       " else cp mkmf/bin/* /usr/local/bin; fi \n"]
 
         # Set bld_dir, src_dir, mkmf_template
         self.bldsetup=["RUN bld_dir="+self.bld+" \\ \n",
diff --git a/fre/make/make_helpers.py b/fre/make/make_helpers.py
index 5ecdc2cb1..73633ffa2 100644
--- a/fre/make/make_helpers.py
+++ b/fre/make/make_helpers.py
@@ -1,6 +1,7 @@
 ''' this holds functions used across various parts of fre/make subtools '''
 
 import logging
+import os
 from pathlib import Path
 from typing import Optional
 
@@ -28,9 +29,26 @@ def get_mktemplate_path(mk_template: str, container_flag: bool, model_root: Opti
     if not container_flag:
         if "/" not in mk_template:
             topdir = Path(__file__).resolve().parents[1]
-            template_path = str(topdir)+ "/mkmf/templates/"+mk_template
+            submodule_path = str(topdir) + "/mkmf/templates/" + mk_template
 
-        # Check in template path exists
+            # First, check the mkmf submodule location (backwards-compatible with both
+            # old mkmf structure and mkmf PR 75, since templates/ stays at repo root)
+            if Path(submodule_path).exists():
+                template_path = submodule_path
+            else:
+                # Fall back to the conda package install location introduced by mkmf PR 75:
+                # templates are installed to $CONDA_PREFIX/share/mkmf/templates/
+                conda_prefix = os.environ.get("CONDA_PREFIX")
+                if conda_prefix:
+                    conda_path = conda_prefix + "/share/mkmf/templates/" + mk_template
+                    if Path(conda_path).exists():
+                        template_path = conda_path
+                    else:
+                        template_path = submodule_path  # use for the error message below
+                else:
+                    template_path = submodule_path  # use for the error message below
+
+        # Check that the resolved template path exists
         if not Path(template_path).exists():
             raise ValueError("Error w/ mkmf template. Created path from given "
                              f"filename: {template_path} does not exist.")
diff --git a/fre/make/tests/test_make_helpers.py b/fre/make/tests/test_make_helpers.py
index b2cd24b28..9bd620425 100644
--- a/fre/make/tests/test_make_helpers.py
+++ b/fre/make/tests/test_make_helpers.py
@@ -1,6 +1,7 @@
 """
 Test fre make make_helpers
 """
+import os
 from pathlib import Path
 import pytest
 from fre.make import make_helpers
@@ -93,3 +94,24 @@ def test_mktemplatepath_dne_with_name(test_variables):
         make_helpers.get_mktemplate_path(mk_template = template_path,
                                          model_root = None,
                                          container_flag = False)
+
+def test_mktemplate_name_conda_prefix(tmp_path, monkeypatch):
+    """
+    Test that the right template_path is constructed from the conda package
+    install location ($CONDA_PREFIX/share/mkmf/templates/) when the mkmf
+    submodule template is not present but the conda package provides it.
+    This covers the mkmf PR 75 backwards-compatible behaviour.
+    """
+    # Create a fake conda prefix with the template installed under share/mkmf/templates/
+    conda_prefix = tmp_path / "conda_env"
+    template_dir = conda_prefix / "share" / "mkmf" / "templates"
+    template_dir.mkdir(parents=True)
+    fake_template = template_dir / "fake-template.mk"
+    fake_template.touch()
+
+    monkeypatch.setenv("CONDA_PREFIX", str(conda_prefix))
+
+    template_path = make_helpers.get_mktemplate_path(mk_template = "fake-template.mk",
+                                                     model_root = None,
+                                                     container_flag = False)
+    assert str(fake_template) == template_path
diff --git a/meta.yaml b/meta.yaml
index 56b556b42..e684ee98a 100644
--- a/meta.yaml
+++ b/meta.yaml
@@ -8,9 +8,32 @@ source:
 build:
   script:
     - {{ PYTHON }} -m pip install . -vv
-    - cp fre/mkmf/bin/mkmf $PREFIX/bin
-    - cp fre/mkmf/bin/list_paths $PREFIX/bin
-    - cp fre/mkmf/bin/git-version-string $PREFIX/bin
+    - |
+      # Backwards-compatible copy of mkmf executables:
+      # mkmf PR 75 moved bin/ to mkmf/bin/ within the mkmf repository,
+      # so the submodule path changed from fre/mkmf/bin/ to fre/mkmf/mkmf/bin/.
+      # Try the new path first, fall back to the old path.
+      # If neither exists, warn but continue (mkmf may be a separate conda dependency).
+      for exe in mkmf list_paths git-version-string; do
+        if [ -f "fre/mkmf/mkmf/bin/$exe" ]; then
+          cp "fre/mkmf/mkmf/bin/$exe" "$PREFIX/bin/$exe"
+        elif [ -f "fre/mkmf/bin/$exe" ]; then
+          cp "fre/mkmf/bin/$exe" "$PREFIX/bin/$exe"
+        else
+          echo "Warning: $exe not found in mkmf submodule (checked fre/mkmf/mkmf/bin/ and fre/mkmf/bin/). Expected to be provided by a separate noaa-gfdl::mkmf conda dependency."
+        fi
+      done
+      # Install mkmf templates to the standard data-files location, mirroring what
+      # mkmf PR 75 does in the standalone mkmf conda package.  This makes fre-cli
+      # self-contained: downstream tools (get_mktemplate_path) resolve a bare
+      # template name to $CONDA_PREFIX/share/mkmf/templates/<name>.mk when the
+      # mkmf submodule templates/ directory is not present at runtime.
+      if [ -d "fre/mkmf/templates" ]; then
+        mkdir -p "$PREFIX/share/mkmf/templates"
+        cp -r fre/mkmf/templates/* "$PREFIX/share/mkmf/templates/"
+      else
+        echo "Warning: fre/mkmf/templates/ not found; mkmf templates not installed to $PREFIX/share/mkmf/templates/."
+      fi
   noarch: python
 
 channels: