diff --git a/docs/changelog/1583.bugfix.rst b/docs/changelog/1583.bugfix.rst
new file mode 100644
index 000000000..aa44088d3
--- /dev/null
+++ b/docs/changelog/1583.bugfix.rst
@@ -0,0 +1,2 @@
+Fix system python discovery mechanism when prefixes contain relative parts (e.g. ``..``) by resolving paths within the
+python information query - by :user:`gaborbernat`.
diff --git a/src/virtualenv/__main__.py b/src/virtualenv/__main__.py
index 12d431a74..b7508203d 100644
--- a/src/virtualenv/__main__.py
+++ b/src/virtualenv/__main__.py
@@ -5,6 +5,8 @@
 import sys
 from datetime import datetime
 
+import six
+
 
 def run(args=None, options=None):
     start = datetime.now()
@@ -14,14 +16,18 @@ def run(args=None, options=None):
     if args is None:
         args = sys.argv[1:]
     try:
-        run_via_cli(args, options)
+        session = run_via_cli(args, options)
+        logging.warning(
+            "created virtual environment in %.0fms %s with seeder %s",
+            (datetime.now() - start).total_seconds() * 1000,
+            six.ensure_text(str(session.creator)),
+            six.ensure_text(str(session.seeder)),
+        )
     except ProcessCallFailed as exception:
         print("subprocess call failed for {}".format(exception.cmd))
         print(exception.out, file=sys.stdout, end="")
         print(exception.err, file=sys.stderr, end="")
         raise SystemExit(exception.code)
-    finally:
-        logging.info("done in %.0fms", (datetime.now() - start).total_seconds() * 1000)
 
 
 def run_with_catch(args=None):
diff --git a/src/virtualenv/discovery/py_info.py b/src/virtualenv/discovery/py_info.py
index 211778c45..8e520ba0d 100644
--- a/src/virtualenv/discovery/py_info.py
+++ b/src/virtualenv/discovery/py_info.py
@@ -35,6 +35,9 @@ def __init__(self):
         def u(v):
             return v.decode("utf-8") if isinstance(v, bytes) else v
 
+        def abs_path(v):
+            return None if v is None else os.path.abspath(v)  # unroll relative elements from path (e.g. ..)
+
         # qualifies the python
         self.platform = u(sys.platform)
         self.implementation = u(platform.python_implementation())
@@ -49,16 +52,16 @@ def u(v):
         self.os = u(os.name)
 
         # information about the prefix - determines python home
-        self.prefix = u(getattr(sys, "prefix", None))  # prefix we think
-        self.base_prefix = u(getattr(sys, "base_prefix", None))  # venv
-        self.real_prefix = u(getattr(sys, "real_prefix", None))  # old virtualenv
+        self.prefix = u(abs_path(getattr(sys, "prefix", None)))  # prefix we think
+        self.base_prefix = u(abs_path(getattr(sys, "base_prefix", None)))  # venv
+        self.real_prefix = u(abs_path(getattr(sys, "real_prefix", None)))  # old virtualenv
 
         # information about the exec prefix - dynamic stdlib modules
-        self.base_exec_prefix = u(getattr(sys, "base_exec_prefix", None))
-        self.exec_prefix = u(getattr(sys, "exec_prefix", None))
+        self.base_exec_prefix = u(abs_path(getattr(sys, "base_exec_prefix", None)))
+        self.exec_prefix = u(abs_path(getattr(sys, "exec_prefix", None)))
 
-        self.executable = u(sys.executable)  # the executable we were invoked via
-        self.original_executable = u(self.executable)  # the executable as known by the interpreter
+        self.executable = u(abs_path(sys.executable))  # the executable we were invoked via
+        self.original_executable = u(abs_path(self.executable))  # the executable as known by the interpreter
         self.system_executable = self._fast_get_system_executable()  # the executable we are based of (if available)
 
         try:
@@ -413,10 +416,6 @@ def _find_possible_folders(self, inside_folder):
 
         # or at root level
         candidate_folder[inside_folder] = None
-        if self.executable.startswith(self.prefix):
-            binary_within = os.path.relpath(os.path.dirname(self.executable), self.prefix)
-            candidate_folder[os.path.join(inside_folder, binary_within)] = None
-
         return list(candidate_folder.keys())
 
     def _find_possible_exe_names(self):
diff --git a/src/virtualenv/run/__init__.py b/src/virtualenv/run/__init__.py
index 309e33b26..ed7f6ef9b 100644
--- a/src/virtualenv/run/__init__.py
+++ b/src/virtualenv/run/__init__.py
@@ -2,8 +2,6 @@
 
 import logging
 
-import six
-
 from ..config.cli.parser import VirtualEnvConfigParser
 from ..report import LEVELS, setup_report
 from ..session import Session
@@ -22,12 +20,6 @@ def run_via_cli(args, options=None):
     """
     session = session_via_cli(args, options)
     session.run()
-
-    logging.warning(
-        "created virtual environment %s with seeder %s",
-        six.ensure_text(str(session.creator)),
-        six.ensure_text(str(session.seeder)),
-    )
     return session