diff --git a/poetry/factory.py b/poetry/factory.py
index 36078bed1e5..144bfe35871 100644
--- a/poetry/factory.py
+++ b/poetry/factory.py
@@ -153,14 +153,15 @@ def configure_sources(
 
             poetry.pool.add_repository(repository, is_default, secondary=is_secondary)
 
-        # Always put PyPI last to prefer private repositories
-        # but only if we have no other default source
-        if not poetry.pool.has_default():
-            has_sources = bool(sources)
-            poetry.pool.add_repository(PyPiRepository(), not has_sources, has_sources)
-        else:
+        # Put PyPI last to prefer private repositories
+        # unless we have no default source AND no primary sources
+        # (default = false, secondary = false)
+        if poetry.pool.has_default():
             if io.is_debug():
                 io.write_line("Deactivating the PyPI repository")
+        else:
+            default = not poetry.pool.has_primary_repositories()
+            poetry.pool.add_repository(PyPiRepository(), default, not default)
 
     @classmethod
     def create_legacy_repository(
diff --git a/poetry/repositories/pool.py b/poetry/repositories/pool.py
index 251ff92506b..b57ba155ec2 100644
--- a/poetry/repositories/pool.py
+++ b/poetry/repositories/pool.py
@@ -25,6 +25,7 @@ def __init__(
         self._lookup: Dict[str, int] = {}
         self._repositories: List[Repository] = []
         self._default = False
+        self._has_primary_repositories = False
         self._secondary_start_idx = None
 
         for repository in repositories:
@@ -41,6 +42,9 @@ def repositories(self) -> List[Repository]:
     def has_default(self) -> bool:
         return self._default
 
+    def has_primary_repositories(self) -> bool:
+        return self._has_primary_repositories
+
     def has_repository(self, name: str) -> bool:
         name = name.lower() if name is not None else None
 
@@ -84,6 +88,7 @@ def add_repository(
             self._repositories.append(repository)
             self._lookup[repository_name] = len(self._repositories) - 1
         else:
+            self._has_primary_repositories = True
             if self._secondary_start_idx is None:
                 self._repositories.append(repository)
                 self._lookup[repository_name] = len(self._repositories) - 1
diff --git a/tests/fixtures/with_non_default_multiple_secondary_sources/pyproject.toml b/tests/fixtures/with_non_default_multiple_secondary_sources/pyproject.toml
new file mode 100644
index 00000000000..933bee96912
--- /dev/null
+++ b/tests/fixtures/with_non_default_multiple_secondary_sources/pyproject.toml
@@ -0,0 +1,24 @@
+[tool.poetry]
+name = "my-package"
+version = "1.2.3"
+description = "Some description."
+authors = [
+    "Your Name <you@example.com>"
+]
+license = "MIT"
+
+# Requirements
+[tool.poetry.dependencies]
+python = "~2.7 || ^3.6"
+
+[tool.poetry.dev-dependencies]
+
+[[tool.poetry.source]]
+name = "foo"
+url = "https://foo.bar/simple/"
+secondary = true
+
+[[tool.poetry.source]]
+name = "bar"
+url = "https://bar.baz/simple/"
+secondary = true
diff --git a/tests/fixtures/with_non_default_multiple_sources/pyproject.toml b/tests/fixtures/with_non_default_multiple_sources/pyproject.toml
new file mode 100644
index 00000000000..6cacb602e8b
--- /dev/null
+++ b/tests/fixtures/with_non_default_multiple_sources/pyproject.toml
@@ -0,0 +1,23 @@
+[tool.poetry]
+name = "my-package"
+version = "1.2.3"
+description = "Some description."
+authors = [
+    "Your Name <you@example.com>"
+]
+license = "MIT"
+
+# Requirements
+[tool.poetry.dependencies]
+python = "~2.7 || ^3.6"
+
+[tool.poetry.dev-dependencies]
+
+[[tool.poetry.source]]
+name = "foo"
+url = "https://foo.bar/simple/"
+secondary = true
+
+[[tool.poetry.source]]
+name = "bar"
+url = "https://bar.baz/simple/"
diff --git a/tests/fixtures/with_non_default_secondary_source/pyproject.toml b/tests/fixtures/with_non_default_secondary_source/pyproject.toml
new file mode 100644
index 00000000000..453e3f9747f
--- /dev/null
+++ b/tests/fixtures/with_non_default_secondary_source/pyproject.toml
@@ -0,0 +1,19 @@
+[tool.poetry]
+name = "my-package"
+version = "1.2.3"
+description = "Some description."
+authors = [
+    "Your Name <you@example.com>"
+]
+license = "MIT"
+
+# Requirements
+[tool.poetry.dependencies]
+python = "~2.7 || ^3.6"
+
+[tool.poetry.dev-dependencies]
+
+[[tool.poetry.source]]
+name = "foo"
+url = "https://foo.bar/simple/"
+secondary = true
diff --git a/tests/test_factory.py b/tests/test_factory.py
index 13a0437174c..e9a9a9a5994 100644
--- a/tests/test_factory.py
+++ b/tests/test_factory.py
@@ -176,6 +176,64 @@ def test_poetry_with_non_default_source():
     assert isinstance(poetry.pool.repositories[1], PyPiRepository)
 
 
+def test_poetry_with_non_default_secondary_source():
+    poetry = Factory().create_poetry(fixtures_dir / "with_non_default_secondary_source")
+
+    assert len(poetry.pool.repositories) == 2
+
+    assert poetry.pool.has_default()
+
+    repository = poetry.pool.repositories[0]
+    assert repository.name == "PyPI"
+    assert isinstance(repository, PyPiRepository)
+
+    repository = poetry.pool.repositories[1]
+    assert repository.name == "foo"
+    assert isinstance(repository, LegacyRepository)
+
+
+def test_poetry_with_non_default_multiple_secondary_sources():
+    poetry = Factory().create_poetry(
+        fixtures_dir / "with_non_default_multiple_secondary_sources"
+    )
+
+    assert len(poetry.pool.repositories) == 3
+
+    assert poetry.pool.has_default()
+
+    repository = poetry.pool.repositories[0]
+    assert repository.name == "PyPI"
+    assert isinstance(repository, PyPiRepository)
+
+    repository = poetry.pool.repositories[1]
+    assert repository.name == "foo"
+    assert isinstance(repository, LegacyRepository)
+
+    repository = poetry.pool.repositories[2]
+    assert repository.name == "bar"
+    assert isinstance(repository, LegacyRepository)
+
+
+def test_poetry_with_non_default_multiple_sources():
+    poetry = Factory().create_poetry(fixtures_dir / "with_non_default_multiple_sources")
+
+    assert len(poetry.pool.repositories) == 3
+
+    assert not poetry.pool.has_default()
+
+    repository = poetry.pool.repositories[0]
+    assert repository.name == "bar"
+    assert isinstance(repository, LegacyRepository)
+
+    repository = poetry.pool.repositories[1]
+    assert repository.name == "foo"
+    assert isinstance(repository, LegacyRepository)
+
+    repository = poetry.pool.repositories[2]
+    assert repository.name == "PyPI"
+    assert isinstance(repository, PyPiRepository)
+
+
 def test_poetry_with_no_default_source():
     poetry = Factory().create_poetry(fixtures_dir / "sample_project")