diff --git a/runtime/drivers/clickhouse/model_manager.go b/runtime/drivers/clickhouse/model_manager.go
index 0a1e167cf2e..efe0e34168c 100644
--- a/runtime/drivers/clickhouse/model_manager.go
+++ b/runtime/drivers/clickhouse/model_manager.go
@@ -180,6 +180,14 @@ func (c *Connection) validateAndApplyDefaults(opts *drivers.ModelExecuteOptions,
 		ip.SQL = ip.SQL + " SETTINGS " + op.QuerySettings
 	}
 
+	if ip != nil {
+		ip.PostExec = strings.TrimSpace(ip.PostExec)
+		ip.PreExec = strings.TrimSpace(ip.PreExec)
+	}
+	if op != nil {
+		op.PostExec = strings.TrimSpace(op.PostExec)
+		op.PreExec = strings.TrimSpace(op.PreExec)
+	}
 	return nil
 }
 
diff --git a/runtime/drivers/duckdb/model_executor_localfile_self.go b/runtime/drivers/duckdb/model_executor_localfile_self.go
index af285fec8c7..f4ab52209bd 100644
--- a/runtime/drivers/duckdb/model_executor_localfile_self.go
+++ b/runtime/drivers/duckdb/model_executor_localfile_self.go
@@ -69,7 +69,7 @@ func (e *localFileToSelfExecutor) Execute(ctx context.Context, opts *drivers.Mod
 		}
 		warnings = append(warnings, fmt.Sprintf("Undefined fields %q in output properties. Will be ignored.", strings.Join(unused, ", ")))
 	}
-	if err := outputProps.validateAndApplyDefaults(opts, &ModelInputProperties{}, outputProps); err != nil {
+	if err := outputProps.validateAndApplyDefaults(opts, &ModelInputProperties{}); err != nil {
 		return nil, fmt.Errorf("invalid output properties: %w", err)
 	}
 
diff --git a/runtime/drivers/duckdb/model_executor_self.go b/runtime/drivers/duckdb/model_executor_self.go
index a3158c2d70a..6aae90720d1 100644
--- a/runtime/drivers/duckdb/model_executor_self.go
+++ b/runtime/drivers/duckdb/model_executor_self.go
@@ -54,7 +54,7 @@ func (e *selfToSelfExecutor) Execute(ctx context.Context, opts *drivers.ModelExe
 		}
 		warnings = append(warnings, fmt.Sprintf("Undefined fields %q in input properties. Will be ignored.", strings.Join(unused, ", ")))
 	}
-	if err := inputProps.Validate(); err != nil {
+	if err := inputProps.ValidateAndApplyDefaults(); err != nil {
 		return nil, fmt.Errorf("invalid input properties: %w", err)
 	}
 
@@ -69,7 +69,7 @@ func (e *selfToSelfExecutor) Execute(ctx context.Context, opts *drivers.ModelExe
 		}
 		warnings = append(warnings, fmt.Sprintf("Undefined fields %q in output properties. Will be ignored.", strings.Join(unused, ", ")))
 	}
-	if err := outputProps.validateAndApplyDefaults(opts, inputProps, outputProps); err != nil {
+	if err := outputProps.validateAndApplyDefaults(opts, inputProps); err != nil {
 		return nil, fmt.Errorf("invalid output properties: %w", err)
 	}
 
diff --git a/runtime/drivers/duckdb/model_executor_self_file.go b/runtime/drivers/duckdb/model_executor_self_file.go
index 7a655710f6b..100cd96bcb2 100644
--- a/runtime/drivers/duckdb/model_executor_self_file.go
+++ b/runtime/drivers/duckdb/model_executor_self_file.go
@@ -46,7 +46,7 @@ func (e *selfToFileExecutor) Execute(ctx context.Context, opts *drivers.ModelExe
 		}
 		warnings = append(warnings, fmt.Sprintf("Undefined fields %q in input properties. Will be ignored.", strings.Join(unused, ", ")))
 	}
-	if err := inputProps.Validate(); err != nil {
+	if err := inputProps.ValidateAndApplyDefaults(); err != nil {
 		return nil, fmt.Errorf("invalid input properties: %w", err)
 	}
 
diff --git a/runtime/drivers/duckdb/model_executor_self_objectstore.go b/runtime/drivers/duckdb/model_executor_self_objectstore.go
index 4b25c1ea6c0..e005920375c 100644
--- a/runtime/drivers/duckdb/model_executor_self_objectstore.go
+++ b/runtime/drivers/duckdb/model_executor_self_objectstore.go
@@ -43,7 +43,7 @@ func (e *selfToObjectStoreExecutor) Execute(ctx context.Context, opts *drivers.M
 		}
 		warnings = append(warnings, fmt.Sprintf("Undefined fields %q in input properties. Will be ignored.", strings.Join(unused, ", ")))
 	}
-	if err := inputProps.Validate(); err != nil {
+	if err := inputProps.ValidateAndApplyDefaults(); err != nil {
 		return nil, fmt.Errorf("invalid input properties: %w", err)
 	}
 
diff --git a/runtime/drivers/duckdb/model_manager.go b/runtime/drivers/duckdb/model_manager.go
index 6133c1e671b..93abf794f82 100644
--- a/runtime/drivers/duckdb/model_manager.go
+++ b/runtime/drivers/duckdb/model_manager.go
@@ -26,7 +26,10 @@ type ModelInputProperties struct {
 	InternalDropSecretSQL   string `mapstructure:"internal_drop_secret_sql"`
 }
 
-func (p *ModelInputProperties) Validate() error {
+func (p *ModelInputProperties) ValidateAndApplyDefaults() error {
+	p.SQL = strings.TrimSpace(p.SQL)
+	p.PreExec = strings.TrimSpace(p.PreExec)
+	p.PostExec = strings.TrimSpace(p.PostExec)
 	if p.SQL == "" {
 		return fmt.Errorf("missing property 'sql'")
 	}
@@ -47,7 +50,7 @@ type ModelOutputProperties struct {
 	CreateSecretsFromConnectors []string `mapstructure:"create_secrets_from_connectors"`
 }
 
-func (p *ModelOutputProperties) validateAndApplyDefaults(opts *drivers.ModelExecuteOptions, ip *ModelInputProperties, op *ModelOutputProperties) error {
+func (p *ModelOutputProperties) validateAndApplyDefaults(opts *drivers.ModelExecuteOptions, ip *ModelInputProperties) error {
 	if opts.Incremental || opts.PartitionRun {
 		if p.Materialize != nil && !*p.Materialize {
 			return fmt.Errorf("incremental or partitioned models must be materialized")
@@ -78,21 +81,23 @@ func (p *ModelOutputProperties) validateAndApplyDefaults(opts *drivers.ModelExec
 
 	// We want to use partition_overwrite as the default incremental strategy for models with partitions.
 	// This requires us to inject the partition key into the SQL query, so this only works for SQL models.
-	if op.IncrementalStrategy == drivers.IncrementalStrategyUnspecified {
-		if len(op.UniqueKey) > 0 {
-			op.IncrementalStrategy = drivers.IncrementalStrategyMerge
+	if p.IncrementalStrategy == drivers.IncrementalStrategyUnspecified {
+		if len(p.UniqueKey) > 0 {
+			p.IncrementalStrategy = drivers.IncrementalStrategyMerge
 		} else if opts.PartitionRun && ip != nil && ip.SQL != "" {
 			ip.SQL = fmt.Sprintf("SELECT %s AS __rill_partition, * FROM (%s\n)", safeSQLString(opts.PartitionKey), ip.SQL)
-			op.IncrementalStrategy = drivers.IncrementalStrategyPartitionOverwrite
-			op.PartitionBy = "__rill_partition"
+			p.IncrementalStrategy = drivers.IncrementalStrategyPartitionOverwrite
+			p.PartitionBy = "__rill_partition"
 		}
 	}
 
 	// If we failed to apply a better incremental strategy, fall back to append.
-	if op.IncrementalStrategy == drivers.IncrementalStrategyUnspecified {
-		op.IncrementalStrategy = drivers.IncrementalStrategyAppend
+	if p.IncrementalStrategy == drivers.IncrementalStrategyUnspecified {
+		p.IncrementalStrategy = drivers.IncrementalStrategyAppend
 	}
 
+	p.PreExec = strings.TrimSpace(p.PreExec)
+	p.PostExec = strings.TrimSpace(p.PostExec)
 	return nil
 }
 
diff --git a/runtime/reconcilers/model_test.go b/runtime/reconcilers/model_test.go
index bb3b0631273..3c768261381 100644
--- a/runtime/reconcilers/model_test.go
+++ b/runtime/reconcilers/model_test.go
@@ -151,7 +151,7 @@ sql: SELECT 1 AS num
 }
 
 func TestPartitionedIncrementalPostExecSeesIncrementalFlag(t *testing.T) {
-	rt, instanceID := testruntime.NewInstance(t)
+	rt, instanceID := testruntime.NewInstanceWithOptions(t, testruntime.InstanceOptions{StageChanges: true})
 
 	testruntime.PutFiles(t, rt, instanceID, map[string]string{
 		"rill.yaml": ``,