diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 74654f0bacb..571c648afc8 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -182,7 +182,7 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==1.4.52 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.25 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index 4360d718181..1879c3437ee 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -68,7 +68,7 @@ install_requires =
     refgenconf>=0.12.0
     regex
     requests
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     sqlitedict
     starlette
     svgwrite
diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
index 157324e102a..3e3e0e085e5 100644
--- a/packages/data/setup.cfg
+++ b/packages/data/setup.cfg
@@ -58,7 +58,7 @@ install_requires =
     pysam>=0.21
     rocrate
     social-auth-core[openidconnect]==4.0.3
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     tifffile
     typing-extensions
     WebOb
diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
index 40c3be56f52..05394dca8e2 100644
--- a/packages/job_execution/setup.cfg
+++ b/packages/job_execution/setup.cfg
@@ -38,7 +38,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     MarkupSafe
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 20ac5878220..53ef0062558 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -58,7 +58,7 @@ install_requires =
     PyYAML
     requests
     Routes
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     sqlalchemy-migrate
     starlette
     starlette-context
diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg
index e04d3f101f3..55d3421dade 100644
--- a/packages/web_framework/setup.cfg
+++ b/packages/web_framework/setup.cfg
@@ -40,7 +40,7 @@ install_requires =
     pydantic>=2,!=2.6.0,!=2.6.1
     requests
     Routes
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
     WebOb
 
 packages = find:
diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg
index f7bc6adc5d5..16e6d08f1c1 100644
--- a/packages/web_stack/setup.cfg
+++ b/packages/web_stack/setup.cfg
@@ -34,7 +34,7 @@ include_package_data = True
 install_requires =
     galaxy-data
     galaxy-util
-    SQLAlchemy>=1.4.25,<2
+    SQLAlchemy>=2.0,<2.1
 packages = find:
 python_requires = >=3.8
 
diff --git a/pyproject.toml b/pyproject.toml
index ae05b3d66db..1829b50f0e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -108,7 +108,7 @@ Routes = "*"
 schema-salad = "!=8.3.20220721194857"  # https://github.com/common-workflow-language/schema_salad/issues/575
 social-auth-core = ">=4.5.0"  # to drop dependency on abandoned python-jose
 sortedcontainers = "*"
-SQLAlchemy = ">=1.4.25,<2"
+SQLAlchemy = "^2.0"
 sqlitedict = "*"
 sqlparse = "*"
 starlette = "*"