diff --git a/enginetest/queries/script_queries.go b/enginetest/queries/script_queries.go
index 22d5e4f1b0..510085e225 100644
--- a/enginetest/queries/script_queries.go
+++ b/enginetest/queries/script_queries.go
@@ -122,6 +122,67 @@ type ScriptTestAssertion struct {
 // Unlike other engine tests, ScriptTests must be self-contained. No other tables are created outside the definition of
 // the tests.
 var ScriptTests = []ScriptTest{
+	{
+		// https://github.com/dolthub/go-mysql-server/issues/3259
+		Dialect: "mysql",
+		Name:    "Missing column with same name as system variable",
+		SetUpScript: []string{
+			"CREATE DATABASE IF NOT EXISTS test_db",
+			"USE test_db",
+			"CREATE TABLE A (id INT)",
+			"CREATE TABLE B (id INT)",
+			"INSERT INTO A VALUES (1)",
+			"INSERT INTO B VALUES (2)",
+		},
+		Assertions: []ScriptTestAssertion{
+			{
+				Query:       "SELECT UNIX_TIMESTAMP(A.timestamp) FROM A LIMIT 1",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT A.timestamp FROM A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT A.version FROM A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT A.max_connections FROM A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT UPPER(A.sql_mode) FROM A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:            "SELECT @@timestamp",
+				Expected:         []sql.Row{{float64(0)}},
+				SkipResultsCheck: true, // dynamic var
+			},
+			{
+				Query:            "SELECT @@version",
+				Expected:         []sql.Row{{""}},
+				SkipResultsCheck: true, // dynamic var
+			},
+			{
+				Query:       "SELECT test_db.A.timestamp FROM A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT test_db.A.version FROM test_db.A",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT a1.timestamp FROM A a1 JOIN B b1 ON a1.id = b1.id",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+			{
+				Query:       "SELECT b1.max_connections FROM A a1 JOIN B b1 ON a1.id = b1.id",
+				ExpectedErr: sql.ErrTableColumnNotFound,
+			},
+		},
+	},
 	{
 		// https://github.com/dolthub/dolt/issues/9927
 		// https://github.com/dolthub/dolt/issues/9053
diff --git a/sql/planbuilder/scalar.go b/sql/planbuilder/scalar.go
index ecf4453211..5d83706230 100644
--- a/sql/planbuilder/scalar.go
+++ b/sql/planbuilder/scalar.go
@@ -126,9 +126,15 @@ func (b *Builder) buildScalar(inScope *scope, e ast.Expr) (ex sql.Expression) {
 			if aliasedExpr, ok := inScope.selectAliases[colName]; ok {
 				return aliasedExpr
 			}
-			sysVar, scope, ok := b.buildSysVar(v, ast.SetScope_None)
-			if ok {
-				return sysVar
+			// Only try system variable lookup if there's no table qualifier.
+			// Qualified names like "A.timestamp" are always column references, never system variables.
+			var scope ast.SetScope
+			if tblName == "" && dbName == "" {
+				var sysVar sql.Expression
+				sysVar, scope, ok = b.buildSysVar(v, ast.SetScope_None)
+				if ok {
+					return sysVar
+				}
 			}
 			var err error
 			if scope == ast.SetScope_User || scope == ast.SetScope_Persist || scope == ast.SetScope_PersistOnly {