diff --git a/src/PackageCompiler.jl b/src/PackageCompiler.jl
index 6fa7a565..89b0f565 100644
--- a/src/PackageCompiler.jl
+++ b/src/PackageCompiler.jl
@@ -296,7 +296,8 @@ function create_fresh_base_sysimage(; cpu_target::String, sysimage_build_args::C
     @static if VERSION >= v"1.12.0-DEV.1617"
         compiler_source_path = joinpath(base_dir, "Base_compiler.jl")
         buildroot = ""
-        dataroot = relpath(joinpath(Sys.BINDIR, Base.DATAROOTDIR), base_dir) * "/"
+        # Use realpath to handle symlinked directories (common in local Julia builds)
+        dataroot = relpath(realpath(joinpath(Sys.BINDIR, Base.DATAROOTDIR)), realpath(base_dir)) * "/"
         compiler_args = `--buildroot $buildroot --dataroot $dataroot` # build path
     else
         compiler_source_path = joinpath(base_dir, "compiler", "compiler.jl")
@@ -948,6 +949,7 @@ function create_app(package_dir::String,
     include_preferences && bundle_preferences(ctx, app_dir)
     bundle_cert(app_dir)
 
+    # Sysimage always goes in lib/julia/ (this is hardcoded in the Julia binary)
     sysimage_path = joinpath(app_dir, "lib", "julia", "sys." * Libdl.dlext)
 
     package_name = ctx.env.pkg.name
@@ -1367,13 +1369,18 @@ function bundle_julia_libraries(dest_dir, stdlibs)
     app_libjulia_dir = Sys.isunix() ? joinpath(app_lib_dir, "julia") : app_lib_dir
     lib_dir = julia_libdir()
     libjulia_dir = Sys.isunix() ? joinpath(lib_dir, "julia") : lib_dir
-    # File structure is slightly different on locally built julias:
-    if !isempty(glob(glob_pattern_lib("libLLVM"), lib_dir))
+    # File structure is different on locally built julias:
+    # libraries are in lib/ directly instead of lib/julia/, and the DEP_LIBS
+    # embedded in libjulia.so reflect this. We must copy libraries to the same
+    # relative location to match the binary's expectations.
+    if is_local_julia_build()
         libjulia_dir = lib_dir
+        app_libjulia_dir = app_lib_dir
     end
 
     mkpath(app_lib_dir)
-    Sys.isunix() && mkpath(app_libjulia_dir)
+    # Always create lib/julia/ for the sysimage (even for local builds where libraries go to lib/)
+    Sys.isunix() && mkpath(joinpath(app_lib_dir, "julia"))
 
     tot_libsize = 0
     printstyled("PackageCompiler: bundled libraries:\n")
diff --git a/src/juliaconfig.jl b/src/juliaconfig.jl
index 66eb1673..4673b1ff 100644
--- a/src/juliaconfig.jl
+++ b/src/juliaconfig.jl
@@ -13,6 +13,13 @@ function julia_libdir()
     return dirname(abspath(Libdl.dlpath(libname)))
 end
 
+# Detect if Julia is a local build (libraries in lib/ directly instead of lib/julia/)
+function is_local_julia_build()
+    lib_dir = julia_libdir()
+    # In local builds, libLLVM is directly in lib/, not in lib/julia/
+    return any(startswith(f, "libLLVM") for f in readdir(lib_dir))
+end
+
 function julia_private_libdir()
     if Base.DARWIN_FRAMEWORK # taken from Libdl tests
         if isdebugbuild() != 0