diff --git a/CMakeLists.txt b/CMakeLists.txt
index c1299b0794..5b8f66af74 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,6 +38,17 @@ else()
     set(QT_MAJOR_VERSION 6)
 endif()
 
+# If MRTRIX_SUBPROJECT_INSTALL_PREFIX is set, it will be used as the install prefix
+# for all targets in this project. This is useful when MRtrix3 is built as a
+# subproject of another project (e.g. via add_subdirectory or FetchContent).
+if(NOT DEFINED MRTRIX_SUBPROJECT_INSTALL_PREFIX)
+    set(MRTRIX_SUBPROJECT_INSTALL_PREFIX "")
+endif()
+set(MRTRIX_INSTALL_BINDIR ${MRTRIX_SUBPROJECT_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR} CACHE INTERNAL "" FORCE)
+set(MRTRIX_INSTALL_LIBDIR ${MRTRIX_SUBPROJECT_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR} CACHE INTERNAL "" FORCE)
+set(MRTRIX_INSTALL_INCLUDEDIR ${MRTRIX_SUBPROJECT_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR} CACHE INTERNAL "" FORCE)
+set(MRTRIX_INSTALL_DATADIR ${MRTRIX_SUBPROJECT_INSTALL_PREFIX}/${CMAKE_INSTALL_DATADIR} CACHE INTERNAL "" FORCE)
+
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -57,8 +68,8 @@ else()
 endif()
 
 file(RELATIVE_PATH relDir
-    ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
-    ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
+    ${CMAKE_CURRENT_BINARY_DIR}/${MRTRIX_INSTALL_BINDIR}
+    ${CMAKE_CURRENT_BINARY_DIR}/${MRTRIX_INSTALL_LIBDIR}
 )
 
 set(CMAKE_INSTALL_RPATH ${base} ${base}/${relDir})
diff --git a/cmd/CMakeLists.txt b/cmd/CMakeLists.txt
index fd6de1b333..99af297692 100644
--- a/cmd/CMakeLists.txt
+++ b/cmd/CMakeLists.txt
@@ -44,8 +44,8 @@ function(add_cmd CMD_SRC IS_GUI)
     endif ()
 
     install(TARGETS ${CMD_NAME}
-        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-        BUNDLE DESTINATION ${CMAKE_INSTALL_BINDIR}
+        RUNTIME DESTINATION ${MRTRIX_INSTALL_BINDIR}
+        BUNDLE DESTINATION ${MRTRIX_INSTALL_BINDIR}
     )
 endfunction()
 
diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
index 7cc54e9388..dc00b03dba 100644
--- a/core/CMakeLists.txt
+++ b/core/CMakeLists.txt
@@ -96,6 +96,6 @@ target_include_directories(mrtrix-core PUBLIC
 )
 
 install(TARGETS mrtrix-core
-    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${MRTRIX_INSTALL_BINDIR}
+    LIBRARY DESTINATION ${MRTRIX_INSTALL_LIBDIR}
 )
diff --git a/python/mrtrix3/CMakeLists.txt b/python/mrtrix3/CMakeLists.txt
index b11c6378bb..99b27384e1 100644
--- a/python/mrtrix3/CMakeLists.txt
+++ b/python/mrtrix3/CMakeLists.txt
@@ -66,10 +66,10 @@ add_custom_target(PythonLibFiles
 
 install(FILES ${PYTHON_LIB_FILES}
     PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-    DESTINATION ${CMAKE_INSTALL_LIBDIR}/mrtrix3
+    DESTINATION ${MRTRIX_INSTALL_LIBDIR}/mrtrix3
 )
 
 install(FILES ${PYTHON_VERSION_FILE}
     PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-    DESTINATION ${CMAKE_INSTALL_LIBDIR}/mrtrix3
+    DESTINATION ${MRTRIX_INSTALL_LIBDIR}/mrtrix3
 )
diff --git a/python/mrtrix3/commands/CMakeLists.txt b/python/mrtrix3/commands/CMakeLists.txt
index f8a37c0343..871af6fd57 100644
--- a/python/mrtrix3/commands/CMakeLists.txt
+++ b/python/mrtrix3/commands/CMakeLists.txt
@@ -63,7 +63,7 @@ foreach(PYTHON_SRC_PATH ${PYTHON_ALL_COMMANDS_FILES})
     get_filename_component(DST_INSTALLDIR ${DST_RELPATH} DIRECTORY)
     install(FILES ${PYTHON_SRC_PATH}
         PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-        DESTINATION ${CMAKE_INSTALL_LIBDIR}/mrtrix3/commands/${DST_INSTALLDIR}
+        DESTINATION ${MRTRIX_INSTALL_LIBDIR}/mrtrix3/commands/${DST_INSTALLDIR}
     )
     list(APPEND PYTHON_BUILD_COMMAND_FILES ${DST_PATH})
 endforeach()
@@ -100,10 +100,10 @@ add_custom_target(PythonCommands
 
 install(FILES ${PYTHON_BIN_FILES}
     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
-    DESTINATION ${CMAKE_INSTALL_BINDIR}
+    DESTINATION ${MRTRIX_INSTALL_BINDIR}
 )
 
 install(FILES ${PYTHON_COMMANDS_INIT_FILE}
     PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-    DESTINATION ${CMAKE_INSTALL_LIBDIR}/mrtrix3/commands/
+    DESTINATION ${MRTRIX_INSTALL_LIBDIR}/mrtrix3/commands/
 )
diff --git a/share/CMakeLists.txt b/share/CMakeLists.txt
index e51beb70eb..e72d899d7b 100644
--- a/share/CMakeLists.txt
+++ b/share/CMakeLists.txt
@@ -5,17 +5,17 @@ add_custom_target(copy-share-data ALL
 )
 
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/mrtrix3/
-    DESTINATION ${CMAKE_INSTALL_DATADIR}/mrtrix3
+    DESTINATION ${MRTRIX_INSTALL_DATADIR}/mrtrix3
 )
 
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/icons/hicolor
-    DESTINATION ${CMAKE_INSTALL_DATADIR}/icons
+    DESTINATION ${MRTRIX_INSTALL_DATADIR}/icons
 )
 
 install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/applications/mrview.desktop
-    DESTINATION ${CMAKE_INSTALL_DATADIR}/applications
+    DESTINATION ${MRTRIX_INSTALL_DATADIR}/applications
 )
 
 install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/mime/mrtrix-mime.xml
-    DESTINATION ${CMAKE_INSTALL_DATADIR}/mime
+    DESTINATION ${MRTRIX_INSTALL_DATADIR}/mime
 )
\ No newline at end of file
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 55c51f5ecd..b894013e04 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -112,13 +112,13 @@ if(WIN32)
 endif()
 
 install(TARGETS mrtrix-headless
-    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${MRTRIX_INSTALL_BINDIR}
+    LIBRARY DESTINATION ${MRTRIX_INSTALL_LIBDIR}
 )
 
 if(MRTRIX_BUILD_GUI)
     install(TARGETS mrtrix-gui
-        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        RUNTIME DESTINATION ${MRTRIX_INSTALL_BINDIR}
+        LIBRARY DESTINATION ${MRTRIX_INSTALL_LIBDIR}
     )
 endif()