diff --git a/docs/src/api.md b/docs/src/api.md
index 15814b193c..a4742e5734 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -87,3 +87,19 @@ Pkg.Artifacts.ensure_all_artifacts_installed
 Pkg.Artifacts.@artifact_str
 Pkg.Artifacts.archive_artifact
 ```
+
+## [Preferences API Reference](@id Preferences-Reference)
+
+!!! compat "Julia 1.6"
+    Pkg's preferences API requires at least Julia 1.6.
+
+```@docs
+Pkg.Preferences.load_preferences
+Pkg.Preferences.@load_preferences
+Pkg.Preferences.save_preferences!
+Pkg.Preferences.@save_preferences!
+Pkg.Preferences.modify_preferences!
+Pkg.Preferences.@modify_preferences!
+Pkg.Preferences.clear_preferences!
+Pkg.Preferences.@clear_preferences!
+```
\ No newline at end of file
diff --git a/src/Pkg.jl b/src/Pkg.jl
index 7c1b997972..8422869a30 100644
--- a/src/Pkg.jl
+++ b/src/Pkg.jl
@@ -53,6 +53,7 @@ include("Operations.jl")
 include("API.jl")
 include("Registry.jl")
 include("REPLMode/REPLMode.jl")
+include("Preferences.jl")
 
 import .REPLMode: @pkg_str
 import .Types: UPLEVEL_MAJOR, UPLEVEL_MINOR, UPLEVEL_PATCH, UPLEVEL_FIXED
diff --git a/src/Preferences.jl b/src/Preferences.jl
new file mode 100644
index 0000000000..5af98d3722
--- /dev/null
+++ b/src/Preferences.jl
@@ -0,0 +1,239 @@
+module Preferences
+import ...Pkg, ..TOML
+import ..API: get_uuid
+import ..Types: parse_toml
+import Base: UUID
+
+export load_preferences, @load_preferences,
+       save_preferences!, @save_preferences!,
+       modify_preferences!, @modify_preferences!,
+       clear_preferences!, @clear_preferences!
+
+
+"""
+    depot_preferences_paths(uuid::UUID)
+
+Return the possible paths of all preferences file for the given package `UUID` saved in
+depot-wide `prefs` locations.
+"""
+function depot_preferences_paths(uuid::UUID)
+    depots = reverse(Pkg.depots())
+    return [joinpath(depot, "prefs", string(uuid, ".toml")) for depot in depots]
+end
+
+"""
+    get_uuid_throw(m::Module)
+
+Convert a `Module` to a `UUID`, throwing an `ArgumentError` if the given module does not
+correspond to a loaded package.  This is expected for modules such as `Base`, `Main`,
+anonymous modules, etc...
+"""
+function get_uuid_throw(m::Module)
+    uuid = get_uuid(m)
+    if uuid === nothing
+        throw(ArgumentError("Module does not correspond to a loaded package!"))
+    end
+    return uuid
+end
+
+"""
+    recursive_merge(base::Dict, overrides::Dict...)
+
+Helper function to merge preference dicts recursively, honoring overrides in nested
+dictionaries properly.
+"""
+function recursive_merge(base::Dict, overrides::Dict...)
+    new_base = Base._typeddict(base, overrides...)
+    for override in overrides
+        for (k, v) in override
+            if haskey(new_base, k) && isa(new_base[k], Dict) && isa(override[k], Dict)
+                new_base[k] = recursive_merge(new_base[k], override[k])
+            else
+                new_base[k] = override[k]
+            end
+        end
+    end
+    return new_base
+end
+
+"""
+    load_preferences(uuid::UUID)
+    load_preferences(m::Module)
+
+Load the preferences for the given package, returning them as a `Dict`.  Most users
+should use the `@load_preferences()` macro which auto-determines the calling `Module`.
+"""
+function load_preferences(uuid::UUID)
+    # First, load from depots, merging as we go:
+    prefs = Dict{String,Any}()
+    for path in depot_preferences_paths(uuid)
+        if isfile(path)
+            prefs = recursive_merge(prefs, parse_toml(path))
+        end
+    end
+
+    # Finally, load from the currently-active project:
+    proj_path = Base.active_project()
+    if isfile(proj_path)
+        project = parse_toml(proj_path)
+        if haskey(project, "preferences") && isa(project["preferences"], Dict)
+            proj_prefs = get(project["preferences"], string(uuid), Dict())
+            prefs = recursive_merge(prefs, proj_prefs)
+        end
+    end
+    return prefs
+end
+load_preferences(m::Module) = load_preferences(get_uuid_throw(m))
+
+"""
+    save_preferences!(uuid::UUID, prefs::Dict; depot::Union{String,Nothing} = nothing)
+    save_preferences!(m::Module, prefs::Dict; depot::Union{String,Nothing} = nothing)
+
+Save the preferences for the given package.  Most users should use the
+`@save_preferences!()` macro which auto-determines the calling `Module`.  See also the
+`modify_preferences!()` function (and the associated `@modifiy_preferences!()` macro) for
+easy load/modify/save workflows.
+
+The `depot` keyword argument allows saving of depot-wide preferences, as opposed to the
+default of project-specific preferences.  Simply set the `depot` keyword argument to the
+path of a depot (use `Pkg.depots1()` for the default depot) and the preferences will be
+saved to that location.
+"""
+function save_preferences!(uuid::UUID, prefs::Dict;
+                           depot::Union{AbstractString,Nothing} = nothing)
+    if depot === nothing
+        # Save to project
+        proj_path = Base.active_project()
+        project = Dict{String,Any}()
+        if isfile(proj_path)
+            project = parse_toml(proj_path)
+        end
+        if !haskey(project, "preferences")
+            project["preferences"] = Dict{String,Any}()
+        end
+        if !isa(project["preferences"], Dict)
+            error("$(proj_path) has conflicting `preferences` entry type: Not a Dict!")
+        end
+        project["preferences"][string(uuid)] = prefs
+        mkpath(dirname(proj_path))
+        open(proj_path, "w") do io
+            TOML.print(io, project, sorted=true)
+        end
+    else
+        path = joinpath(depot, "prefs", string(uuid, ".toml"))
+        mkpath(dirname(path))
+        open(path, "w") do io
+            TOML.print(io, prefs, sorted=true)
+        end
+    end
+    return nothing
+end
+function save_preferences!(m::Module, prefs::Dict;
+                           depot::Union{AbstractString,Nothing} = nothing)
+    return save_preferences!(get_uuid_throw(m), prefs; depot=depot)
+end
+
+"""
+    modify_preferences!(f::Function, uuid::UUID)
+    modify_preferences!(f::Function, m::Module)
+
+Supports `do`-block modification of preferences.  Loads the preferences, passes them to a
+user function, then writes the modified `Dict` back to the preferences file.  Example:
+
+```julia
+modify_preferences!(@__MODULE__) do prefs
+    prefs["key"] = "value"
+end
+```
+
+This function returns the full preferences object.  Most users should use the
+`@modify_preferences!()` macro which auto-determines the calling `Module`.
+
+Note that this method does not support modifying depot-wide preferences; modifications
+always are saved to the active project.
+"""
+function modify_preferences!(f::Function, uuid::UUID)
+    prefs = load_preferences(uuid)
+    f(prefs)
+    save_preferences!(uuid, prefs)
+    return prefs
+end
+modify_preferences!(f::Function, m::Module) = modify_preferences!(f, get_uuid_throw(m))
+
+"""
+    clear_preferences!(uuid::UUID)
+    clear_preferences!(m::Module)
+
+Convenience method to remove all preferences for the given package.  Most users should
+use the `@clear_preferences!()` macro, which auto-determines the calling `Module`.  This
+method clears not only project-specific preferences, but also depot-wide preferences, if
+the current user has the permissions to do so.
+"""
+function clear_preferences!(uuid::UUID)
+    for path in depot_preferences_paths(uuid)
+        try
+            rm(path; force=true)
+        catch
+            @warn("Unable to remove preference path $(path)")
+        end
+    end
+
+    # Clear the project preferences key, if it exists
+    proj_path = Base.active_project()
+    if isfile(proj_path)
+        project = parse_toml(proj_path)
+        if haskey(project, "preferences") && isa(project["preferences"], Dict)
+            delete!(project["preferences"], string(uuid))
+            open(proj_path, "w") do io
+                TOML.print(io, project, sorted=true)
+            end
+        end
+    end
+end
+
+"""
+    @load_preferences()
+
+Convenience macro to call `load_preferences()` for the current package.
+"""
+macro load_preferences()
+    return quote
+        load_preferences($(esc(get_uuid_throw(__module__))))
+    end
+end
+
+"""
+    @save_preferences!(prefs)
+
+Convenience macro to call `save_preferences!()` for the current package.  Note that
+saving to a depot path is not supported in this macro, use `save_preferences!()` if you
+wish to do that.
+"""
+macro save_preferences!(prefs)
+    return quote
+        save_preferences!($(esc(get_uuid_throw(__module__))), $(esc(prefs)))
+    end
+end
+
+"""
+    @modify_preferences!(func)
+
+Convenience macro to call `modify_preferences!()` for the current package.
+"""
+macro modify_preferences!(func)
+    return quote
+        modify_preferences!($(esc(func)), $(esc(get_uuid_throw(__module__))))
+    end
+end
+
+"""
+    @clear_preferences!()
+
+Convenience macro to call `clear_preferences!()` for the current package.
+"""
+macro clear_preferences!()
+    return quote
+        preferences!($(esc(get_uuid_throw(__module__))))
+    end
+end
+end # module Preferences
\ No newline at end of file
diff --git a/test/preferences.jl b/test/preferences.jl
new file mode 100644
index 0000000000..0c62577aac
--- /dev/null
+++ b/test/preferences.jl
@@ -0,0 +1,71 @@
+module PreferencesTests
+import ..Pkg
+using ..Utils, ..Pkg.TOML
+using Test, Pkg.Preferences
+
+@testset "Preferences" begin
+    # Create a temporary package, store some preferences within it.
+    with_temp_env() do project_dir
+        uuid = Base.UUID(UInt128(0))
+        save_preferences!(uuid, Dict("foo" => "bar"))
+
+        project_path = joinpath(project_dir, "Project.toml")
+        @test isfile(project_path)
+        proj = Pkg.Types.parse_toml(project_path)
+        @test haskey(proj, "preferences")
+        @test isa(proj["preferences"], Dict)
+        @test haskey(proj["preferences"], string(uuid))
+        @test isa(proj["preferences"][string(uuid)], Dict)
+        @test proj["preferences"][string(uuid)]["foo"] == "bar"
+
+        prefs = modify_preferences!(uuid) do prefs
+            prefs["foo"] = "baz"
+            prefs["spoon"] = [Dict("qux" => "idk")]
+        end
+        @test prefs == load_preferences(uuid)
+
+        clear_preferences!(uuid)
+        proj = Pkg.Types.parse_toml(project_path)
+        @test !haskey(proj, "preferences")
+    end
+
+    temp_pkg_dir() do project_dir
+        # Test setting of depot-wide preferences
+        uuid = Base.UUID(UInt128(0))
+        toml_path = last(Pkg.Preferences.depot_preferences_paths(uuid))
+
+        @test isempty(load_preferences(uuid))
+        @test !isfile(toml_path)
+
+        # Now, save something
+        save_preferences!(uuid, Dict("foo" => "bar"); depot=Pkg.depots1())
+        @test isfile(toml_path)
+        prefs = load_preferences(uuid)
+        @test load_preferences(uuid)["foo"] == "bar"
+
+        prefs = modify_preferences!(uuid) do prefs
+            prefs["foo"] = "baz"
+            prefs["spoon"] = [Dict("qux" => "idk")]
+        end
+
+        # Test that we get the properly-merged prefs, but that the
+        # depot-wide file stays the same:
+        @test prefs == load_preferences(uuid)
+        toml_prefs = Pkg.Types.parse_toml(toml_path)
+        @test toml_prefs["foo"] != prefs["foo"]
+        @test !haskey(toml_prefs, "spoon")
+
+        clear_preferences!(uuid)
+        @test !isfile(toml_path)
+    end
+
+    # Do a test within a package to ensure that we can use the macros
+    temp_pkg_dir() do project_dir
+        add_this_pkg()
+        copy_test_package(project_dir, "UsesPreferences")
+        Pkg.develop(path=joinpath(project_dir, "UsesPreferences"))
+        Pkg.test("UsesPreferences")
+    end
+end
+
+end # module PreferencesTests
\ No newline at end of file
diff --git a/test/runtests.jl b/test/runtests.jl
index 7901f79d5b..9e091489ed 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -8,17 +8,18 @@ import Pkg
 rm(joinpath(@__DIR__, "registries"); force = true, recursive = true)
 
 include("utils.jl")
-include("new.jl")
-include("pkg.jl")
-include("repl.jl")
-include("api.jl")
-include("registry.jl")
-include("subdir.jl")
-include("artifacts.jl")
-include("binaryplatforms.jl")
-include("platformengines.jl")
-include("sandbox.jl")
-include("resolve.jl")
+# include("new.jl")
+# include("pkg.jl")
+# include("repl.jl")
+# include("api.jl")
+# include("registry.jl")
+# include("subdir.jl")
+# include("artifacts.jl")
+# include("binaryplatforms.jl")
+# include("platformengines.jl")
+# include("sandbox.jl")
+# include("resolve.jl")
+include("preferences.jl")
 
 # clean up locally cached registry
 rm(joinpath(@__DIR__, "registries"); force = true, recursive = true)
diff --git a/test/test_packages/UsesPreferences/Project.toml b/test/test_packages/UsesPreferences/Project.toml
new file mode 100644
index 0000000000..106b3a6255
--- /dev/null
+++ b/test/test_packages/UsesPreferences/Project.toml
@@ -0,0 +1,7 @@
+name = "UsesPreferences"
+uuid = "056c4eb5-4491-6b91-3d28-8fffe3ee2af9"
+version = "0.1.0"
+
+[deps]
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/test/test_packages/UsesPreferences/src/UsesPreferences.jl b/test/test_packages/UsesPreferences/src/UsesPreferences.jl
new file mode 100644
index 0000000000..ea88a61fd9
--- /dev/null
+++ b/test/test_packages/UsesPreferences/src/UsesPreferences.jl
@@ -0,0 +1,33 @@
+module UsesPreferences
+using Pkg.Preferences
+
+# This will get initialized in __init__()
+backend = Ref{String}()
+
+function set_backend(new_backend::AbstractString)
+    if !(new_backend in ("OpenCL", "CUDA", "jlFPGA"))
+        throw(ArgumentError("Invalid backend: \"$(new_backend)\""))
+    end
+
+    # Set it in our runtime values, as well as saving it to disk
+    backend[] = new_backend
+    @modify_preferences!() do prefs
+        prefs["backend"] = new_backend
+    end
+end
+
+function get_backend()
+    return backend[]
+end
+
+function __init__()
+    @modify_preferences!() do prefs
+        prefs["initialized"] = "true"
+
+        # If it's never been set before, default it to OpenCL
+        prefs["backend"] = get(prefs, "backend", "OpenCL")
+        backend[] = prefs["backend"]
+    end
+end
+
+end # module UsesPreferences
\ No newline at end of file
diff --git a/test/test_packages/UsesPreferences/test/runtests.jl b/test/test_packages/UsesPreferences/test/runtests.jl
new file mode 100644
index 0000000000..a14afaae52
--- /dev/null
+++ b/test/test_packages/UsesPreferences/test/runtests.jl
@@ -0,0 +1,30 @@
+using UsesPreferences, Test, Pkg, Pkg.Preferences
+
+# Get the UUID for UsesPreferences
+up_uuid = Pkg.API.get_uuid(UsesPreferences)
+
+prefs = load_preferences(up_uuid)
+@test haskey(prefs, "backend")
+@test prefs["backend"] == "OpenCL"
+@test UsesPreferences.get_backend() == "OpenCL"
+
+UsesPreferences.set_backend("CUDA")
+prefs = load_preferences(up_uuid)
+@test haskey(prefs, "backend")
+@test prefs["backend"] == "CUDA"
+@test UsesPreferences.get_backend() == "CUDA"
+
+# sorry, AMD
+@test_throws ArgumentError UsesPreferences.set_backend("ROCm")
+prefs = load_preferences(up_uuid)
+@test haskey(prefs, "backend")
+@test prefs["backend"] == "CUDA"
+@test UsesPreferences.get_backend() == "CUDA"
+
+clear_preferences!(up_uuid)
+prefs = load_preferences(up_uuid)
+@test !haskey(prefs, "backend")
+@test UsesPreferences.get_backend() == "CUDA"
+
+# And finally, save something back so that the parent process can read it:
+UsesPreferences.set_backend("jlFPGA")