diff --git a/core/config/meta/constants.go b/core/config/meta/constants.go
index 19eebcb50..cc1027f2b 100644
--- a/core/config/meta/constants.go
+++ b/core/config/meta/constants.go
@@ -99,3 +99,12 @@ var DiffusersSchedulerOptions = []FieldOption{
 	{Value: "heun", Label: "Heun"},
 	{Value: "unipc", Label: "UniPC"},
 }
+
+// SystemMessagesAfterFirstOptions are the values of template.system_messages_after_first:
+// how system messages that appear after the first turn are handled before the chat
+// template runs (empty = pass through unchanged, which strict Jinja templates reject).
+var SystemMessagesAfterFirstOptions = []FieldOption{
+	{Value: "", Label: "Pass through (default)"},
+	{Value: "merge", Label: "Merge into the first system message"},
+	{Value: "user", Label: "Forward as user messages"},
+}
diff --git a/core/config/meta/registry.go b/core/config/meta/registry.go
index fbf40fa8b..44447a6d6 100644
--- a/core/config/meta/registry.go
+++ b/core/config/meta/registry.go
@@ -382,6 +382,14 @@ func DefaultRegistry() map[string]FieldMetaOverride {
 			Description: "Use the chat template from the model's tokenizer config",
 			Order:       44,
 		},
+		"template.system_messages_after_first": {
+			Section:     "templates",
+			Label:       "System Messages After First",
+			Description: "How system messages that appear after the first turn are handled before templating: merge into the first system message, or forward as user messages. Empty passes them through unchanged, which strict Jinja templates reject.",
+			Component:   "select",
+			Options:     SystemMessagesAfterFirstOptions,
+			Order:       45,
+		},
 		// Router section template — kept in the templates UI section
 		// (rather than the router section under "other") so operators
 		// editing prompt shapes find all template-typed fields in one
diff --git a/core/config/model_config.go b/core/config/model_config.go
index 600519c7f..ecc234d8c 100644
--- a/core/config/model_config.go
+++ b/core/config/model_config.go
@@ -1351,6 +1351,16 @@ type TemplateConfig struct {
 	// that can use the tokenizers specified in the JSON config files of the models
 	UseTokenizerTemplate bool `yaml:"use_tokenizer_template,omitempty" json:"use_tokenizer_template,omitempty"`
 
+	// SystemMessagesAfterFirst controls what happens to system-role messages that
+	// appear after the leading system block. Some tokenizer chat templates (e.g.
+	// Qwen3.8 / Flash-Next) raise "System message must be at the beginning" for
+	// them, while agent frameworks (cogito tool selection, adjustment prompts)
+	// legitimately append system instructions mid-conversation.
+	//   ""/"error": pass through unchanged (template decides)
+	//   "merge":    fold them into the leading system message
+	//   "user":     forward them as user-role instructions (keeps their position)
+	SystemMessagesAfterFirst string `yaml:"system_messages_after_first,omitempty" json:"system_messages_after_first,omitempty"`
+
 	// JoinChatMessagesByCharacter is a string that will be used to join chat messages together.
 	// It defaults to \n
 	JoinChatMessagesByCharacter *string `yaml:"join_chat_messages_by_character,omitempty" json:"join_chat_messages_by_character,omitempty"`
diff --git a/core/http/endpoints/openai/chat.go b/core/http/endpoints/openai/chat.go
index 72fe59b0e..a5b731d9e 100644
--- a/core/http/endpoints/openai/chat.go
+++ b/core/http/endpoints/openai/chat.go
@@ -66,6 +66,65 @@ func stripEmptySystemMessages(messages []schema.Message) []schema.Message {
 	return out
 }
 
+// normalizeLateSystemMessages handles system-role messages that appear after the
+// leading system block, according to template.system_messages_after_first:
+// "merge" folds them into the first system message (created if absent), "user"
+// forwards them as user-role turns at their original position. Any other value
+// returns the messages unchanged. Needed for tokenizer templates that reject
+// late system turns (Qwen3.8: "System message must be at the beginning") while
+// agent frameworks append instructions mid-conversation.
+func normalizeLateSystemMessages(messages []schema.Message, mode string) []schema.Message {
+	if mode != "merge" && mode != "user" {
+		return messages
+	}
+	lead := 0
+	for lead < len(messages) && messages[lead].Role == "system" {
+		lead++
+	}
+	late := false
+	for _, m := range messages[lead:] {
+		if m.Role == "system" {
+			late = true
+			break
+		}
+	}
+	if !late {
+		return messages
+	}
+	out := make([]schema.Message, 0, len(messages)+1)
+	out = append(out, messages[:lead]...)
+	if mode == "merge" && lead == 0 {
+		out = append(out, schema.Message{Role: "system"})
+	}
+	for _, m := range messages[lead:] {
+		if m.Role != "system" {
+			out = append(out, m)
+			continue
+		}
+		text := strings.TrimSpace(messageText(m))
+		if text == "" {
+			continue
+		}
+		switch mode {
+		case "merge":
+			first := &out[0]
+			joined := strings.TrimSpace(messageText(*first))
+			if joined != "" {
+				joined += "\n\n"
+			}
+			joined += text
+			first.Content = joined
+			first.StringContent = joined
+		case "user":
+			m.Role = "user"
+			m.Content = text
+			m.StringContent = text
+			out = append(out, m)
+		}
+	}
+	return out
+}
+
 // mergeToolCallDeltas merges streaming tool call deltas into complete tool calls.
 // In SSE streaming, a single tool call arrives as multiple chunks sharing the same Index:
 // the first chunk carries the ID, Type, and Name; subsequent chunks append to Arguments.
@@ -182,6 +241,7 @@ func ChatEndpoint(cl *config.ModelConfigLoader, ml *model.ModelLoader, evaluator
 		// Drop blank system turns from the web UI (and similar clients) so they
 		// cannot suppress the model YAML system_prompt / tokenizer defaults.
 		input.Messages = stripEmptySystemMessages(input.Messages)
+		input.Messages = normalizeLateSystemMessages(input.Messages, config.TemplateConfig.SystemMessagesAfterFirst)
 
 		// Tokenizer-template models pass messages through to the backend as-is,
 		// so apply the configured system_prompt when the request did not supply
diff --git a/core/http/endpoints/openai/chat_test.go b/core/http/endpoints/openai/chat_test.go
index 0ef0991dd..6e8aa27f4 100644
--- a/core/http/endpoints/openai/chat_test.go
+++ b/core/http/endpoints/openai/chat_test.go
@@ -378,6 +378,50 @@ var _ = Describe("system message helpers", func() {
 		})
 	})
 
+	Describe("normalizeLateSystemMessages", func() {
+		msgs := func() []schema.Message {
+			return []schema.Message{
+				{Role: "system", Content: "lead", StringContent: "lead"},
+				{Role: "user", Content: "q", StringContent: "q"},
+				{Role: "assistant", Content: "a", StringContent: "a"},
+				{Role: "system", Content: "late", StringContent: "late"},
+				{Role: "user", Content: "q2", StringContent: "q2"},
+			}
+		}
+		It("leaves messages untouched by default", func() {
+			out := normalizeLateSystemMessages(msgs(), "")
+			Expect(out).To(HaveLen(5))
+			Expect(out[3].Role).To(Equal("system"))
+		})
+		It("merge folds late system turns into the leading one", func() {
+			out := normalizeLateSystemMessages(msgs(), "merge")
+			Expect(out).To(HaveLen(4))
+			Expect(out[0].Role).To(Equal("system"))
+			Expect(out[0].StringContent).To(Equal("lead\n\nlate"))
+			for _, m := range out[1:] {
+				Expect(m.Role).NotTo(Equal("system"))
+			}
+		})
+		It("merge creates a leading system message when none exists", func() {
+			in := msgs()[1:]
+			out := normalizeLateSystemMessages(in, "merge")
+			Expect(out[0].Role).To(Equal("system"))
+			Expect(out[0].StringContent).To(Equal("late"))
+			Expect(out).To(HaveLen(4))
+		})
+		It("user forwards late system turns as user turns in place", func() {
+			out := normalizeLateSystemMessages(msgs(), "user")
+			Expect(out).To(HaveLen(5))
+			Expect(out[3].Role).To(Equal("user"))
+			Expect(out[3].StringContent).To(Equal("late"))
+			Expect(out[0].Role).To(Equal("system"))
+		})
+		It("does nothing when no late system turn exists", func() {
+			in := msgs()[:3]
+			Expect(normalizeLateSystemMessages(in, "user")).To(HaveLen(3))
+		})
+	})
+
 	Describe("stripEmptySystemMessages", func() {
 		It("removes blank system turns and keeps the rest", func() {
 			in := []schema.Message{
diff --git a/docs/content/advanced/model-configuration.md b/docs/content/advanced/model-configuration.md
index d629e1be8..44f388bdd 100644
--- a/docs/content/advanced/model-configuration.md
+++ b/docs/content/advanced/model-configuration.md
@@ -674,6 +674,7 @@ Templates use Go templates with [Sprig functions](http://masterminds.github.io/s
 | `template.multimodal` | string | Template for multimodal interactions |
 | `template.reply_prefix` | string | Prefix to add to model replies |
 | `template.use_tokenizer_template` | bool | Use tokenizer's built-in template (vLLM/transformers) |
+| `template.system_messages_after_first` | string | What to do with `system`-role messages that appear after the leading system block: `merge` folds them into the first system message, `user` forwards them as user-role turns at their position. Unset keeps them as-is. Needed for tokenizer templates that reject late system turns (e.g. Qwen3.8) while agent frameworks append instructions mid-conversation. |
 | `template.join_chat_messages_by_character` | string | Character to join chat messages (default: `\n`) |
 
 ### Template Variables