diff --git a/src/Prefix.jl b/src/Prefix.jl
index cc386b97..f327e05a 100644
--- a/src/Prefix.jl
+++ b/src/Prefix.jl
@@ -213,6 +213,16 @@ function symlink_tree(src::AbstractString, dest::AbstractString)
             src_file = joinpath(root, f)
             dest_file = joinpath(dest, relpath(root, src), f)
             if isfile(dest_file)
+                # Ugh, destination file already exists.  If source and destination files
+                # have the same size and SHA256 hash, just move on, otherwise issue a
+                # warning.
+                if filesize(src_file) == filesize(dest_file)
+                    src_file_hash = open(io -> bytes2hex(sha256(io)), src_file, "r")
+                    dest_file_hash = open(io -> bytes2hex(sha256(io)), dest_file, "r")
+                    if src_file_hash == dest_file_hash
+                        continue
+                    end
+                end
                 # Find source artifact that this pre-existent destination file belongs to
                 dest_artifact_source = realpath(dest_file)
                 while occursin("artifacts", dest_artifact_source) && basename(dirname(dest_artifact_source)) != "artifacts"
diff --git a/test/prefix.jl b/test/prefix.jl
index bf99f951..9d23b233 100644
--- a/test/prefix.jl
+++ b/test/prefix.jl
@@ -159,6 +159,34 @@ end
         @test String(read(joinpath(dstdir, "sym_fileC"))) == "fileC\n"
         @test_throws Base.IOError realpath(joinpath(dstdir, "sym_fileB"))
     end
+
+    @testset "Warnings about clashing files" begin
+        mktempdir() do tmpdir
+            # Create fake source directory
+            srcdir = joinpath(tmpdir, "src")
+            mkdir(srcdir)
+            # Write two files inside the source directory
+            srcfile1 = joinpath(srcdir, "file1")
+            text = "Lorem ipsum dolor sit amet, consectetur adipiscing elit.\n"
+            write(srcfile1, text)
+            srcfile2 = joinpath(srcdir, "file2")
+            write(srcfile2, text ^ 2)
+
+            # Create the destination directory
+            destdir = joinpath(tmpdir, "dest")
+            mkdir(destdir)
+            destfile1 = joinpath(destdir, "file1")
+            # Same text as file1 in the source directory
+            write(destfile1, text)
+            destfile2 = joinpath(destdir, "file2")
+            # Different text from file2 in the source directory
+            write(destfile2, text)
+
+            # Set up a symlink tree inside of destdir: make sure only the warning about file2 is issued
+            @test_logs (:warn, "Symlink file2 from artifact src already exists in artifact file2") BinaryBuilderBase.symlink_tree(srcdir, destdir)
+            BinaryBuilderBase.unsymlink_tree(srcdir, destdir)
+        end
+    end
 end
 
 @testset "Compression" begin