diff --git a/.github/workflows/end-to-end-test-macos.yml b/.github/workflows/end-to-end-test-macos.yml
index 7d396810..faf1db3e 100644
--- a/.github/workflows/end-to-end-test-macos.yml
+++ b/.github/workflows/end-to-end-test-macos.yml
@@ -79,14 +79,14 @@ jobs:
           export CPPFLAGS="-I/usr/local/opt/llvm@16/include"
           cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE="$(pwd)/build/conan_toolchain.cmake" -DUSE_PARALLEL=true -DRUN_EXPENSIVE_TESTS=false -DENABLE_EXPENSIVE_CHECKS=true -DCMAKE_CXX_COMPILER=clang++ -DADDITIONAL_COMPILER_FLAGS="-fexperimental-library" -DADDITIONAL_LINKER_FLAGS="-L$(brew --prefix llvm)/lib/c++"
           source build/conanrun.sh
-          make -C build ServerMain IndexBuilderMain
+          make -C build qlever-server qlever-index
 
       - name: Check that qlever binaries and qlever script are found and work
         run: |
           export PATH="$PATH:$(pwd)/qlever-code/build"
           source qlever-code/build/conanrun.sh
-          ServerMain --help | head -3; echo "..."
-          IndexBuilderMain --help | head -3; echo "..."
+          qlever-server --help | head -3; echo "..."
+          qlever-index --help | head -3; echo "..."
           qlever --help
 
       - name: Test qlever script for olympics dataset, without Docker
diff --git a/.github/workflows/end-to-end-test-ubuntu.yml b/.github/workflows/end-to-end-test-ubuntu.yml
index aa62a1f1..0173892a 100644
--- a/.github/workflows/end-to-end-test-ubuntu.yml
+++ b/.github/workflows/end-to-end-test-ubuntu.yml
@@ -50,17 +50,17 @@ jobs:
           git pull
           mkdir -p build && cd $_
           cmake -DCMAKE_BUILD_TYPE=Release -DLOGLEVEL=INFO -DUSE_PARALLEL=true -GNinja ..
-          ninja ServerMain IndexBuilderMain
+          ninja qlever-server qlever-index
           docker pull adfreiburg/qlever
 
       - name: Check that qlever binaries, docker image, and qlever script are found and work
         run: |
           mkdir qlever-indices
           export PATH="$PATH:$(pwd)/qlever-control:$(pwd)/qlever-code/build"
-          docker run --entrypoint bash adfreiburg/qlever -c "ServerMain --help" | head -3
-          docker run --entrypoint bash adfreiburg/qlever -c "IndexBuilderMain --help" | head -3
-          ServerMain --help | head -3; echo "..."
-          IndexBuilderMain --help | head -3; echo "..."
+          docker run --entrypoint bash adfreiburg/qlever -c "qlever-server --help" | head -3
+          docker run --entrypoint bash adfreiburg/qlever -c "qlever-index --help" | head -3
+          qlever-server --help | head -3; echo "..."
+          qlever-index --help | head -3; echo "..."
           qlever --help
 
       - name: Test qlever script for olympics dataset, with docker
diff --git a/pyproject.toml b/pyproject.toml
index e9b281c7..785e6620 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "qlever"
 description = "Command-line tool for using the QLever graph database"
-version = "0.5.43"
+version = "0.5.44"
 authors = [
     { name = "Hannah Bast", email = "bast@cs.uni-freiburg.de" }
 ]
diff --git a/src/qlever/Qleverfiles/Qleverfile.default b/src/qlever/Qleverfiles/Qleverfile.default
index eb452b2e..dc4075f3 100644
--- a/src/qlever/Qleverfiles/Qleverfile.default
+++ b/src/qlever/Qleverfiles/Qleverfile.default
@@ -36,7 +36,7 @@ ACCESS_TOKEN =
 
 # Use SYSTEM = docker to run QLever inside a docker container; the Docker image
 # will be downloaded automatically. Use SYSTEM = native to use self-compiled
-# binaries `IndexBuilderMain` and `ServerMain` (which should be in you PATH).
+# binaries `qlever-index` and `qlever-server` (which should be in you PATH).
 [runtime]
 SYSTEM = docker
 IMAGE  = docker.io/adfreiburg/qlever:latest
diff --git a/src/qlever/commands/add_text_index.py b/src/qlever/commands/add_text_index.py
index 6aa67e77..6735c722 100644
--- a/src/qlever/commands/add_text_index.py
+++ b/src/qlever/commands/add_text_index.py
@@ -5,7 +5,7 @@
 from qlever.command import QleverCommand
 from qlever.containerize import Containerize
 from qlever.log import log
-from qlever.util import get_existing_index_files, run_command
+from qlever.util import binary_exists, get_existing_index_files, run_command
 
 
 class AddTextIndexCommand(QleverCommand):
@@ -82,14 +82,7 @@ def execute(self, args) -> bool:
 
         # When running natively, check if the binary exists and works.
         if args.system == "native":
-            try:
-                run_command(f"{args.index_binary} --help")
-            except Exception as e:
-                log.error(
-                    f'Running "{args.index_binary}" failed ({e}), '
-                    f"set `--index-binary` to a different binary or "
-                    f"use `--container_system`"
-                )
+            if not binary_exists(args.index_binary, "index-binary"):
                 return False
 
         # Check if text index files already exist.
diff --git a/src/qlever/commands/start.py b/src/qlever/commands/start.py
index 4dfb0aac..67944c01 100644
--- a/src/qlever/commands/start.py
+++ b/src/qlever/commands/start.py
@@ -47,7 +47,7 @@ def construct_command(args) -> str:
 # Kill existing server on the same port. Trust that StopCommand() works?
 # Maybe return StopCommand().execute(args) and handle it with a try except?
 def kill_existing_server(args) -> bool:
-    args.cmdline_regex = f"^ServerMain.* -p {args.port}"
+    args.cmdline_regex = f"^qlever-server.* -p {args.port}"
     args.no_containers = True
     if not StopCommand().execute(args):
         log.error("Stopping the existing server failed")
@@ -185,7 +185,7 @@ def execute(self, args) -> bool:
         # TODO: This is currently disabled because I never used it once over
         # the past weeks and it is not clear to me what the use case is.
         if False:  # or args.kill_existing_with_same_name:
-            args.cmdline_regex = f"^ServerMain.* -i {args.name}"
+            args.cmdline_regex = f"^qlever-server.* -i {args.name}"
             args.no_containers = True
             StopCommand().execute(args)
             log.info("")
@@ -234,7 +234,7 @@ def execute(self, args) -> bool:
             )
 
             # Show output of status command.
-            args.cmdline_regex = f"^ServerMain.* -p *{args.port}"
+            args.cmdline_regex = f"^qlever-server.* -p *{args.port}"
             log.info("")
             StatusCommand().execute(args)
             return False
diff --git a/src/qlever/commands/status.py b/src/qlever/commands/status.py
index a8efed54..0f778338 100644
--- a/src/qlever/commands/status.py
+++ b/src/qlever/commands/status.py
@@ -25,7 +25,7 @@ def relevant_qleverfile_arguments(self) -> dict[str: list[str]]:
 
     def additional_arguments(self, subparser) -> None:
         subparser.add_argument("--cmdline-regex",
-                               default="^(ServerMain|IndexBuilderMain)",
+                               default="^(qlever-server|qlever-index)",
                                help="Show only processes where the command "
                                     "line matches this regex")
 
diff --git a/src/qlever/commands/stop.py b/src/qlever/commands/stop.py
index a68d433b..c8ead215 100644
--- a/src/qlever/commands/stop.py
+++ b/src/qlever/commands/stop.py
@@ -45,7 +45,7 @@ def relevant_qleverfile_arguments(self) -> dict[str: list[str]]:
 
     def additional_arguments(self, subparser) -> None:
         subparser.add_argument("--cmdline-regex",
-                               default="ServerMain.* -i [^ ]*%%NAME%%",
+                               default="qlever-server.* -i [^ ]*%%NAME%%",
                                help="Show only processes where the command "
                                     "line matches this regex")
         subparser.add_argument("--no-containers", action="store_true",
@@ -84,7 +84,7 @@ def execute(self, args) -> bool:
         message = "No matching process found" if args.no_containers else \
             "No matching process or container found"
         log.error(message)
-        args.cmdline_regex = "^ServerMain.* -i [^ ]*"
+        args.cmdline_regex = "^qlever-server.* -i [^ ]*"
         log.info("")
         StatusCommand().execute(args)
         return True
diff --git a/src/qlever/config.py b/src/qlever/config.py
index a9b4bdf5..dd6d48a1 100644
--- a/src/qlever/config.py
+++ b/src/qlever/config.py
@@ -220,4 +220,14 @@ def add_qleverfile_option(parser):
                             "arguments on the command line. This is possible, "
                             "but not recommended.")
 
+        # Warn if the old binary names are still being used.
+        if "IndexBuilderMain" in getattr(args, "index_binary", ""):
+            log.warning("The index binary has been renamed from "
+                        "`IndexBuilderMain` to `qlever-index`. Please update "
+                        "your Qleverfile or other configuration.")
+        if "ServerMain" in getattr(args, "server_binary", ""):
+            log.warning("The server binary has been renamed from "
+                        "`ServerMain` to `qlever-server`. Please update "
+                        "your Qleverfile or other configuration.")
+
         return args
diff --git a/src/qlever/qleverfile.py b/src/qlever/qleverfile.py
index cdb62eb4..b713fdbd 100644
--- a/src/qlever/qleverfile.py
+++ b/src/qlever/qleverfile.py
@@ -165,7 +165,7 @@ def arg(*args, **kwargs):
         index_args["index_binary"] = arg(
             "--index-binary",
             type=str,
-            default="IndexBuilderMain",
+            default="qlever-index",
             help="The binary for building the index (this requires "
             "that you have compiled QLever on your machine)",
         )
@@ -242,7 +242,7 @@ def arg(*args, **kwargs):
         server_args["server_binary"] = arg(
             "--server-binary",
             type=str,
-            default="ServerMain",
+            default="qlever-server",
             help="The binary for starting the server (this requires "
             "that you have compiled QLever on your machine)",
         )
diff --git a/src/qlever/util.py b/src/qlever/util.py
index 7b54923f..76c2d08a 100644
--- a/src/qlever/util.py
+++ b/src/qlever/util.py
@@ -326,6 +326,14 @@ def binary_exists(binary: str, cmd_arg: str) -> bool:
         )
         log.info("")
         log.info(f"The error message was: {e}")
+        if binary == "qlever-index" or binary == "qlever-server":
+            log.info("")
+            log.warning(
+                f"This might be because you are using a newer version of "
+                f"the `qlever` command-line tool together with an older "
+                f"Docker image; in that case update with "
+                f"`docker pull adfreiburg/qlever` "
+            )
         return False
 
 
diff --git a/test/qlever/commands/test_start_execute.py b/test/qlever/commands/test_start_execute.py
index 46591c43..10a209a3 100644
--- a/test/qlever/commands/test_start_execute.py
+++ b/test/qlever/commands/test_start_execute.py
@@ -397,7 +397,7 @@ def test_execute_fails_due_to_existing_server(
         args.kill_existing_with_same_port = False
         args.port = "localhorst"
         args.port = 1234
-        args.cmdline_regex = f"^ServerMain.* -p {args.port}"
+        args.cmdline_regex = f"^qlever-server.* -p {args.port}"
         args.no_containers = True
         args.server_binary = "/test/path/server_binary"
         args.name = "TestName"
diff --git a/test/qlever/commands/test_status_execute.py b/test/qlever/commands/test_status_execute.py
index 7f993c81..56a2edb3 100644
--- a/test/qlever/commands/test_status_execute.py
+++ b/test/qlever/commands/test_status_execute.py
@@ -9,7 +9,7 @@
 
 def get_mock_args(only_show):
     args = MagicMock()
-    args.cmdline_regex = "^(ServerMain|IndexBuilderMain)"
+    args.cmdline_regex = "^(qlever-server|qlever-index)"
     args.show = only_show
     return [args, args.cmdline_regex, args.show]
 
diff --git a/test/qlever/commands/test_status_other_methods.py b/test/qlever/commands/test_status_other_methods.py
index c1954000..430a53bc 100644
--- a/test/qlever/commands/test_status_other_methods.py
+++ b/test/qlever/commands/test_status_other_methods.py
@@ -31,7 +31,7 @@ def test_additional_arguments(self):
         args = parser.parse_args([])
 
         # Test that the default value is set correctly
-        self.assertEqual(args.cmdline_regex, "^(ServerMain|IndexBuilderMain)")
+        self.assertEqual(args.cmdline_regex, "^(qlever-server|qlever-index)")
 
         # Test that the help text is correctly set
         argument_help = subparser._group_actions[-1].help
diff --git a/test/qlever/commands/test_stop_execute.py b/test/qlever/commands/test_stop_execute.py
index 41090172..b037d3fb 100644
--- a/test/qlever/commands/test_stop_execute.py
+++ b/test/qlever/commands/test_stop_execute.py
@@ -20,7 +20,7 @@ def test_execute_no_matching_processes_or_containers(
     ):
         # Setup args
         args = MagicMock()
-        args.cmdline_regex = "ServerMain.* -i [^ ]*%%NAME%%"
+        args.cmdline_regex = "qlever-server.* -i [^ ]*%%NAME%%"
         args.name = "TestName"
         args.no_containers = True
         args.server_container = "test_container"
@@ -61,7 +61,7 @@ def test_execute_with_matching_process(
     ):
         # Setup args
         args = MagicMock()
-        args.cmdline_regex = "ServerMain.* -i [^ ]*%%NAME%%"
+        args.cmdline_regex = "qlever-server.* -i [^ ]*%%NAME%%"
         args.name = "TestName"
         args.no_containers = True
         args.server_container = "test_container"
@@ -75,7 +75,7 @@ def test_execute_with_matching_process(
         # to test with real psutil.process objects use this:
 
         mock_process.as_dict.return_value = {
-            "cmdline": ["ServerMain", "-i", "/some/path/TestName"],
+            "cmdline": ["qlever-server", "-i", "/some/path/TestName"],
             "pid": 1234,
             "username": "test_user",
         }
@@ -115,7 +115,7 @@ def test_execute_with_containers(
     ):
         # Setup args
         args = MagicMock()
-        args.cmdline_regex = "ServerMain.* -i [^ ]*%%NAME%%"
+        args.cmdline_regex = "qlever-server.* -i [^ ]*%%NAME%%"
         args.name = "TestName"
         args.no_containers = False
         args.server_container = "test_container"
@@ -157,7 +157,7 @@ def test_execute_with_no_containers_and_no_matching_process(
     ):
         # Setup args
         args = MagicMock()
-        args.cmdline_regex = "ServerMain.* -i [^ ]*%%NAME%%"
+        args.cmdline_regex = "qlever-server.* -i [^ ]*%%NAME%%"
         args.name = "TestName"
         args.no_containers = False
         args.server_container = "test_container"
@@ -204,7 +204,7 @@ def test_execute_with_error_killing_process(
     ):
         # Setup args
         args = MagicMock()
-        args.cmdline_regex = "ServerMain.* -i [^ ]*%%NAME%%"
+        args.cmdline_regex = "qlever-server.* -i [^ ]*%%NAME%%"
         args.name = "TestName"
         args.no_containers = True
         args.server_container = "test_container"
@@ -216,7 +216,7 @@ def test_execute_with_error_killing_process(
         # Creating mock psutil.Process objects with necessary attributes
         mock_process = MagicMock()
         mock_process.as_dict.return_value = {
-            "cmdline": ["ServerMain", "-i", "/some/path/TestName"],
+            "cmdline": ["qlever-server", "-i", "/some/path/TestName"],
             "pid": 1234,
             "create_time": 1234567890,
             "memory_info": MagicMock(rss=1024 * 1024 * 512),
diff --git a/test/qlever/commands/test_stop_other_methods.py b/test/qlever/commands/test_stop_other_methods.py
index 7675788b..b69d7b40 100644
--- a/test/qlever/commands/test_stop_other_methods.py
+++ b/test/qlever/commands/test_stop_other_methods.py
@@ -38,7 +38,7 @@ def test_additional_arguments(self):
         args = parser.parse_args([])
 
         # Test that the default value for cmdline_regex is set correctly
-        self.assertEqual(args.cmdline_regex, "ServerMain.* -i [^ ]*%%NAME%%")
+        self.assertEqual(args.cmdline_regex, "qlever-server.* -i [^ ]*%%NAME%%")
 
         # Test that the help text for cmdline_regex is correctly set
         argument_help = subparser._group_actions[-2].help