diff --git a/src/Preferences.jl b/src/Preferences.jl
index 1065b71..3eb28b3 100644
--- a/src/Preferences.jl
+++ b/src/Preferences.jl
@@ -135,7 +135,8 @@ function set_preferences!(target_toml::String, pkg_name::String, pairs::Pair{Str
         d = Base.parsed_toml(target_toml)
     end
     prefs = d
-    if endswith(target_toml, "Project.toml")
+    is_project_toml = endswith(target_toml, "Project.toml")
+    if is_project_toml
         if !haskey(prefs, "preferences")
             prefs["preferences"] = Dict{String,Any}()
         end
@@ -158,11 +159,34 @@ function set_preferences!(target_toml::String, pkg_name::String, pairs::Pair{Str
         prefs[pkg_name] = process_sentinel_values!(prefs[pkg_name])
     end
     open(target_toml, "w") do io
-        TOML.print(io, d, sorted=true)
+        if is_project_toml
+            project_toml_print(io, d)
+        else
+            TOML.print(io, d; sorted=true)
+        end
     end
     return nothing
 end
 
+# Taken from Pkg.jl v1.11.4 (but we don't want to depend on Pkg.jl directly just for this)
+#   https://github.com/JuliaLang/Pkg.jl/blob/v1.11.4/src/project.jl#L235
+# with `preferences` added before `deps`
+const _project_key_order = ["name", "uuid", "keywords", "license", "desc", "preferences", "deps", "weakdeps", "sources", "extensions", "compat"]
+project_key_order(key::String) = something(findfirst(x -> x == key, _project_key_order), length(_project_key_order) + 1)
+function project_toml_print(io::IO, d::Dict)
+    @static if VERSION <= v"1.11-"
+        TOML.print(io, d; sorted=true, by=key -> (project_key_order(key), key))
+    else
+        kw = (sorted=true, by=key -> (project_key_order(key), key))
+        if haskey(d, "sources")
+            inline_tables = IdSet{Dict{String}}(v for v in values(d["sources"]))
+            kw = merge(kw, (; inline_tables))
+        end
+        TOML.print(io, d; kw...)
+    end
+end
+
+
 """
     set_preferences!(uuid_or_module_or_name_or_tuple, prefs::Pair{String,Any}...;
                      export_prefs=false, active_project_only=true, force=false)
diff --git a/test/PkgV_1_11_plus/LocalPkg/Project.toml b/test/PkgV_1_11_plus/LocalPkg/Project.toml
new file mode 100644
index 0000000..05cf645
--- /dev/null
+++ b/test/PkgV_1_11_plus/LocalPkg/Project.toml
@@ -0,0 +1,4 @@
+name = "LocalPkg"
+uuid = "8fa365b9-38ac-4f5f-96f8-37668e8e369e"
+authors = ["Preferences.jl contributors"]
+version = "0.1.0"
diff --git a/test/PkgV_1_11_plus/LocalPkg/src/LocalPkg.jl b/test/PkgV_1_11_plus/LocalPkg/src/LocalPkg.jl
new file mode 100644
index 0000000..42feb00
--- /dev/null
+++ b/test/PkgV_1_11_plus/LocalPkg/src/LocalPkg.jl
@@ -0,0 +1,5 @@
+module LocalPkg
+
+greet() = print("Hello World!")
+
+end # module LocalPkg
diff --git a/test/PkgV_1_11_plus/Project-reference-after.toml b/test/PkgV_1_11_plus/Project-reference-after.toml
new file mode 100644
index 0000000..929b2b7
--- /dev/null
+++ b/test/PkgV_1_11_plus/Project-reference-after.toml
@@ -0,0 +1,26 @@
+name = "PkgV_1_11_plus"
+uuid = "6fde81da-fe91-40db-985f-5f1fb79db309"
+authors = ["Preferences.jl contributors"]
+version = "0.1.0"
+
+[preferences.PkgV_1_11_plus]
+TEST_PREF = true
+
+[deps]
+Example = "7876af07-990d-54b4-ab0e-23690620f79a"
+LocalPkg = "fcf55292-0d03-4e8a-9e0b-701580031fc3"
+
+[sources]
+Example = {url = "https://github.com/JuliaLang/Example.jl"}
+LocalPkg = {path = "LocalPkg"}
+
+[compat]
+Example = "0.5"
+Test = "1.11.0"
+julia = "1.11"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/PkgV_1_11_plus/Project-reference-before.toml b/test/PkgV_1_11_plus/Project-reference-before.toml
new file mode 100644
index 0000000..e1bc92c
--- /dev/null
+++ b/test/PkgV_1_11_plus/Project-reference-before.toml
@@ -0,0 +1,23 @@
+name = "PkgV_1_11_plus"
+uuid = "6fde81da-fe91-40db-985f-5f1fb79db309"
+authors = ["Preferences.jl contributors"]
+version = "0.1.0"
+
+[deps]
+Example = "7876af07-990d-54b4-ab0e-23690620f79a"
+LocalPkg = "fcf55292-0d03-4e8a-9e0b-701580031fc3"
+
+[sources]
+Example = {url = "https://github.com/JuliaLang/Example.jl"}
+LocalPkg = {path = "LocalPkg"}
+
+[compat]
+Example = "0.5"
+Test = "1.11.0"
+julia = "1.11"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/PkgV_1_11_plus/Project.toml b/test/PkgV_1_11_plus/Project.toml
new file mode 100644
index 0000000..e1bc92c
--- /dev/null
+++ b/test/PkgV_1_11_plus/Project.toml
@@ -0,0 +1,23 @@
+name = "PkgV_1_11_plus"
+uuid = "6fde81da-fe91-40db-985f-5f1fb79db309"
+authors = ["Preferences.jl contributors"]
+version = "0.1.0"
+
+[deps]
+Example = "7876af07-990d-54b4-ab0e-23690620f79a"
+LocalPkg = "fcf55292-0d03-4e8a-9e0b-701580031fc3"
+
+[sources]
+Example = {url = "https://github.com/JuliaLang/Example.jl"}
+LocalPkg = {path = "LocalPkg"}
+
+[compat]
+Example = "0.5"
+Test = "1.11.0"
+julia = "1.11"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/test/PkgV_1_11_plus/src/PkgV_1_11_plus.jl b/test/PkgV_1_11_plus/src/PkgV_1_11_plus.jl
new file mode 100644
index 0000000..35a98b3
--- /dev/null
+++ b/test/PkgV_1_11_plus/src/PkgV_1_11_plus.jl
@@ -0,0 +1,5 @@
+module PkgV_1_11_plus
+
+greet() = print("Hello World!")
+
+end # module PkgV_1_11_plus
diff --git a/test/runtests.jl b/test/runtests.jl
index 631be05..ca1a43d 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -444,3 +444,28 @@ end
         end
     end
 end
+
+# https://github.com/JuliaPackaging/Preferences.jl/issues/52
+# Need v1.11+ for Project.toml `[sources]` section to be supported.
+if VERSION > v"1.11.0-"
+@testset "Project.toml writing" begin
+    Pkg.activate("PkgV_1_11_plus") do
+        @eval using PkgV_1_11_plus
+        proj_path = joinpath("PkgV_1_11_plus", "Project.toml")
+        proj_before = read(proj_path, String)
+        ref_before = read(joinpath("PkgV_1_11_plus", "Project-reference-before.toml"), String)
+        @test proj_before == ref_before
+        try
+            set_preferences!(PkgV_1_11_plus, "TEST_PREF" => true; export_prefs=true)
+            proj_after = read(proj_path, String)
+            ref_after = read(joinpath("PkgV_1_11_plus", "Project-reference-after.toml"), String)
+            @assert ref_before != ref_after
+            @test proj_after == ref_after
+        finally
+            open(proj_path, "w") do io
+                write(io, proj_before)
+            end
+        end
+    end
+end
+end # if VERSION