diff --git a/.gitignore b/.gitignore
index 58230fb..b3995a1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -76,6 +76,9 @@ htmlcov/
 # Docker
 .dockerignore
 
+# Package 3 — SQLite databases
+data/
+
 # Misc
 *.bak
 *.tmp
diff --git a/backend/.env.example b/backend/.env.example
index 42558be..72c025b 100644
--- a/backend/.env.example
+++ b/backend/.env.example
@@ -14,4 +14,8 @@ CHUNK_OVERLAP=200
 RETRIEVAL_N_RESULTS=10
 RELEVANCE_THRESHOLD=7.0
 
+# SQLite databases (Package 3)
+PROMPTS_DB_PATH=./data/prompts.db
+HISTORY_DB_PATH=./data/history.db
+
 CORS_ORIGINS=["http://localhost:5173","http://localhost:3000"]
diff --git a/backend/app/core/config.py b/backend/app/core/config.py
index e4fc90a..bab6b88 100644
--- a/backend/app/core/config.py
+++ b/backend/app/core/config.py
@@ -22,6 +22,10 @@ class Settings(BaseSettings):
     # Chunk PDF storage (extracted PDF pages)
     document_chunk_path: str = "./document_chunk"
 
+    # SQLite databases (Package 3)
+    prompts_db_path: str = "./data/prompts.db"
+    history_db_path: str = "./data/history.db"
+
     # App configuration moved to settings for easier testing/configuration
     # Cross-origin settings and chunking parameters (Phase 1 plan)
     cors_origins: list[str] = ["http://localhost:5173", "http://localhost:3000"]
diff --git a/backend/app/core/sqlite_db.py b/backend/app/core/sqlite_db.py
new file mode 100644
index 0000000..322c605
--- /dev/null
+++ b/backend/app/core/sqlite_db.py
@@ -0,0 +1,145 @@
+import logging
+import os
+import sqlite3
+from pathlib import Path
+
+from app.core.config import get_settings
+
+logger = logging.getLogger(__name__)
+
+# ── Seed prompt templates (from current hardcoded service prompts) ──────────
+
+_SEED_DECOMPOSE = (
+    "Given this question: '{question}'\n\n"
+    "Break it down into 2-5 simplified sub-questions that would help "
+    "search for relevant information. Each sub-question should be short "
+    "and focused on one aspect. Return as a JSON array of strings."
+)
+
+_SEED_FILTER = (
+    "Given question '{question}' and these document chunks, rate each 0-10 for relevance. "
+    "Return JSON array of scores.\n{chunks}\n"
+)
+
+_SEED_GENERATE = (
+    "Question: {question}\n\n"
+    "Answer the question using ONLY these document chunks. "
+    "Do not use any external knowledge. "
+    "Format your answer as bullet points. "
+    "Cite your sources inline using the exact bracket labels provided, "
+    "e.g. [filename, page N]. Place the citation at the end of each relevant point.\n\n"
+    "Document chunks:\n{context}\n\n"
+    "Answer:"
+)
+
+_SEED_PROFILES = [
+    ("A", 1),
+    ("B", 0),
+    ("C", 0),
+]
+
+_SEED_STEPS = ["decompose", "filter", "generate"]
+_SEED_TEMPLATES = {
+    "decompose": _SEED_DECOMPOSE,
+    "filter": _SEED_FILTER,
+    "generate": _SEED_GENERATE,
+}
+
+# ── Connection factories ────────────────────────────────────────────────────
+
+def _get_db(db_path: str) -> sqlite3.Connection:
+    os.makedirs(os.path.dirname(db_path), exist_ok=True)
+    conn = sqlite3.connect(db_path)
+    conn.row_factory = sqlite3.Row
+    conn.execute("PRAGMA journal_mode=WAL")
+    conn.execute("PRAGMA foreign_keys=ON")
+    return conn
+
+
+def get_prompts_db() -> sqlite3.Connection:
+    return _get_db(get_settings().prompts_db_path)
+
+
+def get_history_db() -> sqlite3.Connection:
+    return _get_db(get_settings().history_db_path)
+
+
+# ── Table initialization ────────────────────────────────────────────────────
+
+def init_prompts_db(conn: sqlite3.Connection) -> None:
+    conn.execute("""
+        CREATE TABLE IF NOT EXISTS system_prompt_profiles (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            name TEXT NOT NULL UNIQUE,
+            is_active INTEGER DEFAULT 0,
+            created_at TEXT NOT NULL DEFAULT (datetime('now')),
+            updated_at TEXT NOT NULL DEFAULT (datetime('now'))
+        )
+    """)
+    conn.execute("""
+        CREATE TABLE IF NOT EXISTS system_prompts (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            profile_id INTEGER NOT NULL,
+            step_name TEXT NOT NULL,
+            prompt_template TEXT NOT NULL,
+            created_at TEXT NOT NULL DEFAULT (datetime('now')),
+            updated_at TEXT NOT NULL DEFAULT (datetime('now')),
+            FOREIGN KEY (profile_id) REFERENCES system_prompt_profiles(id) ON DELETE CASCADE,
+            UNIQUE(profile_id, step_name)
+        )
+    """)
+    conn.commit()
+    logger.info("Prompts DB tables initialized.")
+
+
+def init_history_db(conn: sqlite3.Connection) -> None:
+    conn.execute("""
+        CREATE TABLE IF NOT EXISTS query_history (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            input_text TEXT NOT NULL,
+            extracted_questions TEXT DEFAULT NULL,
+            decomposer_time_ms INTEGER DEFAULT 0,
+            retriever_time_ms INTEGER DEFAULT 0,
+            chunks_retrieved INTEGER DEFAULT 0,
+            filter_time_ms INTEGER DEFAULT 0,
+            chunks_filtered INTEGER DEFAULT 0,
+            generator_time_ms INTEGER DEFAULT 0,
+            total_time_ms INTEGER DEFAULT 0,
+            final_answer TEXT DEFAULT NULL,
+            sources TEXT DEFAULT NULL,
+            profile_used TEXT DEFAULT NULL,
+            created_at TEXT NOT NULL DEFAULT (datetime('now'))
+        )
+    """)
+    conn.execute("""
+        CREATE INDEX IF NOT EXISTS idx_query_history_created_at
+        ON query_history(created_at DESC)
+    """)
+    conn.commit()
+    logger.info("History DB tables initialized.")
+
+
+# ── Seed data ───────────────────────────────────────────────────────────────
+
+def seed_default_profiles(conn: sqlite3.Connection) -> None:
+    for profile_name, is_active in _SEED_PROFILES:
+        inserted = conn.execute(
+            "INSERT OR IGNORE INTO system_prompt_profiles (name, is_active) VALUES (?, ?)",
+            (profile_name, is_active),
+        )
+        if inserted.rowcount == 0:
+            continue
+
+        profile_id = conn.execute(
+            "SELECT id FROM system_prompt_profiles WHERE name=?",
+            (profile_name,),
+        ).fetchone()["id"]
+
+        for step in _SEED_STEPS:
+            conn.execute(
+                "INSERT OR IGNORE INTO system_prompts (profile_id, step_name, prompt_template) VALUES (?, ?, ?)",
+                (profile_id, step, _SEED_TEMPLATES[step]),
+            )
+
+    conn.commit()
+    logger.info("Default profiles (A/B/C) seeded.")
diff --git a/backend/app/main.py b/backend/app/main.py
index e630eb6..42cfb5a 100644
--- a/backend/app/main.py
+++ b/backend/app/main.py
@@ -8,6 +8,13 @@ from fastapi.middleware.cors import CORSMiddleware
 
 from app.routers import ingest, query, documents
 from app.core.config import get_settings
+from app.core.sqlite_db import (
+    get_prompts_db,
+    get_history_db,
+    init_prompts_db,
+    init_history_db,
+    seed_default_profiles,
+)
 
 # Configure logging before app initialization
 LOG_DIR = Path(__file__).parent / "log"
@@ -46,6 +53,15 @@ app.include_router(ingest.router, prefix="/api/v1")
 app.include_router(query.router, prefix="/api/v1")
 app.include_router(documents.router, prefix="/api/v1")
 
+_prompts_conn = get_prompts_db()
+init_prompts_db(_prompts_conn)
+seed_default_profiles(_prompts_conn)
+_prompts_conn.close()
+
+_history_conn = get_history_db()
+init_history_db(_history_conn)
+_history_conn.close()
+
 
 @app.get("/health")
 def health_check():
diff --git a/backend/app/test/test_phase3_sqlite_db.py b/backend/app/test/test_phase3_sqlite_db.py
new file mode 100644
index 0000000..bd56ec3
--- /dev/null
+++ b/backend/app/test/test_phase3_sqlite_db.py
@@ -0,0 +1,381 @@
+"""Tests for Package 3.1 SQLite infrastructure — prompts.db + history.db.
+
+Covers: connection factories, WAL mode, foreign keys, table creation, seed data, idempotency.
+Uses tmp_path for isolated test databases — no real filesystem pollution.
+"""
+
+import sqlite3
+
+import pytest
+
+
+# ── Helpers ────────────────────────────────────────────────────────────────
+
+DEFAULT_PROMPTS_DB = "/tmp/test_prompts.db"
+DEFAULT_HISTORY_DB = "/tmp/test_history.db"
+
+
+def _patch_settings(monkeypatch, prompts_path: str, history_path: str):
+    """Patch Settings to use test-specific DB paths."""
+    monkeypatch.setenv("PROMPTS_DB_PATH", prompts_path)
+    monkeypatch.setenv("HISTORY_DB_PATH", history_path)
+    from app.core.config import get_settings
+    get_settings.cache_clear()
+
+
+# ── Config Tests ───────────────────────────────────────────────────────────
+
+def test_config_default_db_paths(monkeypatch):
+    """New config fields should have sensible defaults."""
+    monkeypatch.delenv("PROMPTS_DB_PATH", raising=False)
+    monkeypatch.delenv("HISTORY_DB_PATH", raising=False)
+
+    from app.core.config import Settings
+
+    settings = Settings()
+    assert settings.prompts_db_path == "./data/prompts.db"
+    assert settings.history_db_path == "./data/history.db"
+
+
+def test_config_db_paths_from_env(tmp_path, monkeypatch):
+    """DB paths should be configurable via environment variables."""
+    prompts_path = str(tmp_path / "my_prompts.db")
+    history_path = str(tmp_path / "my_history.db")
+    monkeypatch.setenv("PROMPTS_DB_PATH", prompts_path)
+    monkeypatch.setenv("HISTORY_DB_PATH", history_path)
+
+    from app.core.config import Settings
+
+    settings = Settings()
+    assert settings.prompts_db_path == prompts_path
+    assert settings.history_db_path == history_path
+
+
+# ── Connection Factory Tests ───────────────────────────────────────────────
+
+def test_get_prompts_db_creates_file_and_dir(tmp_path, monkeypatch):
+    """get_prompts_db() should create the DB file and any missing parent dirs."""
+    prompts_path = str(tmp_path / "subdir" / "prompts.db")
+    history_path = str(tmp_path / "subdir" / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db
+
+    conn = get_prompts_db()
+    assert conn is not None
+    import os
+    assert os.path.isfile(prompts_path)
+    conn.close()
+
+
+def test_get_history_db_creates_file_and_dir(tmp_path, monkeypatch):
+    """get_history_db() should create the DB file and any missing parent dirs."""
+    prompts_path = str(tmp_path / "subdir" / "prompts.db")
+    history_path = str(tmp_path / "subdir" / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_history_db
+
+    conn = get_history_db()
+    assert conn is not None
+    import os
+    assert os.path.isfile(history_path)
+    conn.close()
+
+
+def test_wal_mode_enabled(tmp_path, monkeypatch):
+    """WAL journal mode should be enabled for better concurrency."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db
+
+    conn = get_prompts_db()
+    result = conn.execute("PRAGMA journal_mode").fetchone()
+    assert result[0].upper() == "WAL"
+    conn.close()
+
+
+def test_foreign_keys_enabled(tmp_path, monkeypatch):
+    """Foreign key enforcement should be enabled."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db
+
+    conn = get_prompts_db()
+    result = conn.execute("PRAGMA foreign_keys").fetchone()
+    assert result[0] == 1
+    conn.close()
+
+
+def test_row_factory_is_row(tmp_path, monkeypatch):
+    """Row factory should be sqlite3.Row for dict-like access."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db
+
+    conn = get_prompts_db()
+    assert conn.row_factory is sqlite3.Row
+    conn.close()
+
+
+# ── Table Creation Tests ───────────────────────────────────────────────────
+
+def test_init_prompts_db_creates_tables(tmp_path, monkeypatch):
+    """init_prompts_db() should create system_prompt_profiles + system_prompts tables."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+
+    tables = conn.execute(
+        "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+    ).fetchall()
+    table_names = {t["name"] for t in tables}
+    assert "system_prompt_profiles" in table_names
+    assert "system_prompts" in table_names
+    conn.close()
+
+
+def test_init_prompts_db_idempotent(tmp_path, monkeypatch):
+    """Calling init_prompts_db() twice should not raise errors."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    init_prompts_db(conn)  # second call — must not raise
+    conn.close()
+
+
+def test_init_history_db_creates_table_and_index(tmp_path, monkeypatch):
+    """init_history_db() should create query_history table + created_at index."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_history_db, init_history_db
+
+    conn = get_history_db()
+    init_history_db(conn)
+
+    tables = conn.execute(
+        "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+    ).fetchall()
+    table_names = {t["name"] for t in tables}
+    assert "query_history" in table_names
+
+    indexes = conn.execute(
+        "SELECT name FROM sqlite_master WHERE type='index' ORDER BY name"
+    ).fetchall()
+    index_names = {i["name"] for i in indexes}
+    assert "idx_query_history_created_at" in index_names
+    conn.close()
+
+
+def test_init_history_db_idempotent(tmp_path, monkeypatch):
+    """Calling init_history_db() twice should not raise errors."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_history_db, init_history_db
+
+    conn = get_history_db()
+    init_history_db(conn)
+    init_history_db(conn)  # second call — must not raise
+    conn.close()
+
+
+# ── Seed Data Tests ────────────────────────────────────────────────────────
+
+def test_seed_default_profiles_creates_three_profiles(tmp_path, monkeypatch):
+    """seed_default_profiles() should insert exactly 3 profiles: A, B, C."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+
+    rows = conn.execute(
+        "SELECT name, is_active FROM system_prompt_profiles ORDER BY id"
+    ).fetchall()
+    assert len(rows) == 3
+    names = [r["name"] for r in rows]
+    assert names == ["A", "B", "C"]
+    conn.close()
+
+
+def test_seed_default_profiles_A_is_active(tmp_path, monkeypatch):
+    """Profile A should be active (is_active=1), B and C inactive (is_active=0)."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+
+    profile_a = conn.execute(
+        "SELECT name, is_active FROM system_prompt_profiles WHERE name='A'"
+    ).fetchone()
+    profile_b = conn.execute(
+        "SELECT name, is_active FROM system_prompt_profiles WHERE name='B'"
+    ).fetchone()
+    profile_c = conn.execute(
+        "SELECT name, is_active FROM system_prompt_profiles WHERE name='C'"
+    ).fetchone()
+
+    assert profile_a["is_active"] == 1
+    assert profile_b["is_active"] == 0
+    assert profile_c["is_active"] == 0
+    conn.close()
+
+
+def test_seed_default_profiles_creates_nine_prompts(tmp_path, monkeypatch):
+    """seed_default_profiles() should insert 9 prompt rows (3 profiles × 3 steps)."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+
+    rows = conn.execute(
+        """SELECT sp.step_name, spp.name AS profile_name
+           FROM system_prompts sp
+           JOIN system_prompt_profiles spp ON sp.profile_id = spp.id
+           ORDER BY spp.name, sp.step_name"""
+    ).fetchall()
+    assert len(rows) == 9
+
+    # Each profile should have all 3 steps
+    for profile in ("A", "B", "C"):
+        profile_rows = [r for r in rows if r["profile_name"] == profile]
+        steps = {r["step_name"] for r in profile_rows}
+        assert steps == {"decompose", "filter", "generate"}
+    conn.close()
+
+
+def test_seed_default_profiles_contains_expected_templates(tmp_path, monkeypatch):
+    """Templates should contain expected placeholders for each step."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+
+    # Decompose must have {question}
+    decompose_row = conn.execute(
+        """SELECT sp.prompt_template
+           FROM system_prompts sp
+           JOIN system_prompt_profiles spp ON sp.profile_id = spp.id
+           WHERE spp.name='A' AND sp.step_name='decompose'"""
+    ).fetchone()
+    assert decompose_row is not None
+    assert "{question}" in decompose_row["prompt_template"]
+
+    # Filter must have {question} and {chunks}
+    filter_row = conn.execute(
+        """SELECT sp.prompt_template
+           FROM system_prompts sp
+           JOIN system_prompt_profiles spp ON sp.profile_id = spp.id
+           WHERE spp.name='A' AND sp.step_name='filter'"""
+    ).fetchone()
+    assert filter_row is not None
+    assert "{question}" in filter_row["prompt_template"]
+    assert "{chunks}" in filter_row["prompt_template"]
+
+    # Generate must have {question} and {context}
+    generate_row = conn.execute(
+        """SELECT sp.prompt_template
+           FROM system_prompts sp
+           JOIN system_prompt_profiles spp ON sp.profile_id = spp.id
+           WHERE spp.name='A' AND sp.step_name='generate'"""
+    ).fetchone()
+    assert generate_row is not None
+    assert "{question}" in generate_row["prompt_template"]
+    assert "{context}" in generate_row["prompt_template"]
+
+    conn.close()
+
+
+def test_seed_default_profiles_idempotent(tmp_path, monkeypatch):
+    """Calling seed_default_profiles() twice should not duplicate rows."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+    seed_default_profiles(conn)
+
+    profile_count = conn.execute(
+        "SELECT COUNT(*) FROM system_prompt_profiles"
+    ).fetchone()[0]
+    prompt_count = conn.execute(
+        "SELECT COUNT(*) FROM system_prompts"
+    ).fetchone()[0]
+
+    assert profile_count == 3
+    assert prompt_count == 9
+    conn.close()
+
+
+def test_all_three_profiles_have_identical_seed_templates(tmp_path, monkeypatch):
+    """All 3 profiles should start with identical seed templates."""
+    prompts_path = str(tmp_path / "prompts.db")
+    history_path = str(tmp_path / "history.db")
+    _patch_settings(monkeypatch, prompts_path, history_path)
+
+    from app.core.sqlite_db import get_prompts_db, init_prompts_db, seed_default_profiles
+
+    conn = get_prompts_db()
+    init_prompts_db(conn)
+    seed_default_profiles(conn)
+
+    for step in ("decompose", "filter", "generate"):
+        rows = conn.execute(
+            """SELECT spp.name, sp.prompt_template
+               FROM system_prompts sp
+               JOIN system_prompt_profiles spp ON sp.profile_id = spp.id
+               WHERE sp.step_name = ?
+               ORDER BY spp.name""",
+            (step,),
+        ).fetchall()
+
+        templates = [r["prompt_template"] for r in rows]
+        # All 3 must match
+        assert templates[0] == templates[1] == templates[2], (
+            f"Step '{step}' templates differ across profiles: {templates}"
+        )
+
+    conn.close()