diff --git a/rapids-cmake/cmake/support_conda_env.cmake b/rapids-cmake/cmake/support_conda_env.cmake
index 09571255..622a73d3 100644
--- a/rapids-cmake/cmake/support_conda_env.cmake
+++ b/rapids-cmake/cmake/support_conda_env.cmake
@@ -1,5 +1,5 @@
 #=============================================================================
-# Copyright (c) 2021-2024, NVIDIA CORPORATION.
+# Copyright (c) 2021-2025, NVIDIA CORPORATION.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -41,6 +41,14 @@ the behavior of conda when it builds projects.
 The `target_name` target will add the required compile flags to ensure debug builds
 are generated with `-O0` instead of the conda env default of `-O2`.
 
+.. versionadded:: v25.06.00
+
+The flag `-ffile-prefix-map` is now passed to remap absolute paths starting
+with `$ENV{PREFIX}` to paths relative to it in binaries generated via
+compilation. This ensures paths baked into binaries are relative to the
+environment prefix. This prevents Conda from rewriting these paths when the
+package is installed.
+
 Also offers the ability to modify :cmake:variable:`CMAKE_PREFIX_PATH <cmake:variable:CMAKE_PREFIX_PATH>` to
 include the following paths based on the current conda environment:
 
@@ -164,6 +172,14 @@ function(rapids_cmake_support_conda_env target)
                             "$<HOST_LINK:SHELL:LINKER:-rpath-link=$ENV{BUILD_PREFIX}/lib>")
       endif()
 
+      # For built binaries (like libraries), remap environment absolute paths (`$PREFIX/<path>`) to
+      # paths relative to the environment `$PREFIX` (`<path>`).
+      target_compile_options(${target}
+                             INTERFACE "$<$<COMPILE_LANGUAGE:C>:-ffile-prefix-map=$ENV{PREFIX}/=''>"
+                                       "$<$<COMPILE_LANGUAGE:CXX>:-ffile-prefix-map=$ENV{PREFIX}/=''>"
+                                       "$<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-ffile-prefix-map=$ENV{PREFIX}/=''>"
+      )
+
       if(modify_prefix_path)
         message(VERBOSE "Conda build detected")
         set(prefix_paths "$ENV{PREFIX}" "$ENV{BUILD_PREFIX}")