diff --git a/crates/ecstore/src/set_disk.rs b/crates/ecstore/src/set_disk/mod.rs
similarity index 100%
rename from crates/ecstore/src/set_disk.rs
rename to crates/ecstore/src/set_disk/mod.rs
diff --git a/crates/ecstore/src/store.rs b/crates/ecstore/src/store/mod.rs
similarity index 100%
rename from crates/ecstore/src/store.rs
rename to crates/ecstore/src/store/mod.rs
diff --git a/docs/architecture/migration-progress.md b/docs/architecture/migration-progress.md
index 9a25c8ac3..2985f6570 100644
--- a/docs/architecture/migration-progress.md
+++ b/docs/architecture/migration-progress.md
@@ -5,18 +5,20 @@ Status values: `[ ]` not started, `[~]` in progress, `[x]` complete, `[!]` block
 ## Current Context
 
 - Issue: [`rustfs/backlog#660`](https://github.com/rustfs/backlog/issues/660)
-- Branch: `overtrue/arch-config-model-phase`
+- Branch: `overtrue/arch-ecstore-store-set-disk-layout`
 - Baseline: completed `C-011/C-012/C-013/API-055/API-059/API-079/API-080/API-081/API-082/API-083/API-084/API-085/API-086/API-087/API-088/API-089/API-090/API-091/API-092/API-093/API-094/API-095/API-096/API-097/API-098/API-099/API-100/API-101/API-102/API-103/API-104/API-105/API-106/API-107/API-108/API-109/API-110/API-111/API-112/API-113/API-114/API-115/API-116/API-117/API-118/API-119/API-120/API-121/API-122/API-123/API-124/API-125/API-126/API-127/API-128/API-129/API-130/API-131/API-132/API-133/API-134/API-135/API-136/API-137/API-138/API-139/API-140/API-141/API-142/API-143/API-144/API-145/API-146/API-147/API-148/API-149/API-150/API-151/API-152/API-153/API-154/API-155/API-156/API-157/API-158/API-159/API-160/API-161/API-162/API-163/API-164/API-165/API-166/API-167/API-168/API-169/API-170/API-171/API-172/API-173/API-174/API-175/API-176/API-177/API-178/API-179/API-180/API-181/API-182/API-183/API-184/API-185/API-186/API-187/API-188/API-189/API-190/API-191/API-192/API-193/API-194/API-195/API-196/API-197/API-198/API-199/API-200/API-201/API-202/API-203/API-204/API-205/API-206/API-207/API-208/API-209/API-210/API-211/API-212/API-213/API-214/API-215/API-216/API-217/API-218/API-219/API-220/API-221/API-222/API-223/API-224/API-225/API-226/API-227/API-228/API-229/API-230/API-231/API-232/API-233/API-234/API-235/API-236/API-237/API-238/API-239/API-240/API-241/API-242/API-243/API-244/API-245/API-246/API-247/API-248/API-249/API-250/API-251/API-252/API-253/API-254/CTX-002`.
-- Current baseline also includes API-255 from PR #3923 and API-256 from PR
-  #3925.
-- Current phase PR: CFG-009 config model ownership guard closure.
-- Based on: current `origin/main` after PR #3922 and PR #3925 merged.
-- PR type for this branch: `ci-gate`
-- Runtime behavior changes: none expected for CFG-009; this is a
-  loss-prevention guard and documentation closure for the completed config
-  model ownership migration.
-- Rust code changes: none expected.
-- CI/script changes: lock completed config model ownership against restoring
+- Current baseline also includes API-255 from PR #3923, API-256 from PR
+  #3925, and CFG-009 from PR #3927.
+- Current phase PR: E-017/E-STORE-001 ECStore store and set-disk directory
+  owner layout.
+- Based on: current `origin/main` after PR #3927 merged.
+- PR type for this branch: `pure-move`
+- Runtime behavior changes: none expected for E-017; this is a pure module file
+  move that keeps the existing `store` and `set_disk` module paths.
+- Rust code changes: move ECStore `store.rs` and `set_disk.rs` into their
+  directory module owners without function-body changes.
+- CI/script changes: reject restoring ECStore root `store.rs` or `set_disk.rs`;
+  lock completed config model ownership against restoring
   old `rustfs_ecstore::config` model/accessor compatibility paths, and lock
   ECStore public facades against re-exporting the moved server-config symbols;
   retain the existing completed owner and test/fuzz boundaries against
@@ -49,7 +51,8 @@ Status values: `[ ]` not started, `[~]` in progress, `[x]` complete, `[!]` block
   root SSE re-exports after API-255, reject direct external
   `rustfs_ecstore::api` facade imports outside local `storage_api` boundary
   files after API-256, and reject restoring old ECStore server-config model or
-  global accessor compatibility paths after CFG-009.
+  global accessor compatibility paths after CFG-009, and reject restoring
+  ECStore root `store.rs` or `set_disk.rs` after E-017.
 
 ## Phase 0 Tasks
 
@@ -3881,6 +3884,22 @@ Status values: `[ ]` not started, `[~]` in progress, `[x]` complete, `[!]` block
     formatting, diff hygiene, Rust risk scan, branch freshness check,
     pre-commit quality gate, and three-expert review.
 
+- [x] `E-017/E-STORE-001` Move ECStore store and set-disk roots into directory modules.
+  - Do: move `crates/ecstore/src/store.rs` to
+    `crates/ecstore/src/store/mod.rs` and `crates/ecstore/src/set_disk.rs` to
+    `crates/ecstore/src/set_disk/mod.rs` while preserving the existing module
+    names, submodule wiring, and public crate paths.
+  - Acceptance: `crate::store` and `crate::set_disk` continue to resolve
+    through the same module names, existing submodules stay under their owner
+    directories, and migration rules reject restoring the old root files.
+  - Must preserve: ECStore object/list/multipart/bucket/heal/rebalance
+    orchestration, set-disk read/write/heal/lock/multipart/metadata flows,
+    public API re-exports, object placement, quorum behavior, reader behavior,
+    and all runtime side effects.
+  - Verification: focused ECStore compile/tests, migration and layer guards,
+    formatting, diff hygiene, Rust risk scan, branch freshness check,
+    pre-commit quality gate, and three-expert review.
+
 - [x] `API-129` Route RustFS internal ECStore consumers through owner boundary.
   - Do: expose crate-local ECStore facade module aliases from
     `rustfs/src/storage/mod.rs` and migrate RustFS startup, server, capacity,
@@ -5735,6 +5754,9 @@ Status values: `[ ]` not started, `[~]` in progress, `[x]` complete, `[!]` block
 
 | Expert | Status | Notes |
 |---|---|---|
+| Quality/architecture | pass | E-017 moves ECStore store and set-disk root owners into directory modules and adds a guard against restoring the old root files. |
+| Migration preservation | pass | `crate::store` and `crate::set_disk` module names stay stable, and the staged Rust diff is two 100% renames with no added Rust lines. |
+| Testing/verification | pass | ECStore compile/tests, architecture/layer guards, formatting, diff hygiene, diff-added Rust risk scan, branch freshness, and pre-commit passed. |
 | Quality/architecture | pass | CFG-009 closes the completed config model ownership phase with one guard over old ECStore config compatibility paths and ECStore facade re-exports. |
 | Migration preservation | pass | The slice only adds guard/documentation coverage; ECStore still owns persistence, storage-class state, default wiring, and startup initialization. |
 | Testing/verification | pass | Shell syntax, architecture migration guard, config residual scans, diff hygiene, script/docs risk review, and full PR gate passed. |
diff --git a/scripts/check_architecture_migration_rules.sh b/scripts/check_architecture_migration_rules.sh
index a7f955a88..b5f070f29 100755
--- a/scripts/check_architecture_migration_rules.sh
+++ b/scripts/check_architecture_migration_rules.sh
@@ -130,6 +130,7 @@ EXTERNAL_TEST_ECSTORE_COMPAT_BYPASS_HITS_FILE="${TMP_DIR}/external_test_ecstore_
 FUZZ_ECSTORE_COMPAT_BYPASS_HITS_FILE="${TMP_DIR}/fuzz_ecstore_compat_bypass_hits.txt"
 EXTERNAL_ECSTORE_API_BOUNDARY_HITS_FILE="${TMP_DIR}/external_ecstore_api_boundary_hits.txt"
 LEGACY_ECSTORE_CONFIG_MODEL_HITS_FILE="${TMP_DIR}/legacy_ecstore_config_model_hits.txt"
+ECSTORE_ROOT_STORE_SET_DISK_MODULE_HITS_FILE="${TMP_DIR}/ecstore_root_store_set_disk_module_hits.txt"
 ALL_STORAGE_COMPAT_SELF_FACADE_PATH_HITS_FILE="${TMP_DIR}/all_storage_compat_self_facade_path_hits.txt"
 RUSTFS_LOCAL_COMPAT_OWNER_SELF_PATH_HITS_FILE="${TMP_DIR}/rustfs_local_compat_owner_self_path_hits.txt"
 RUSTFS_ROOT_COMPAT_RELATIVE_CONSUMER_HITS_FILE="${TMP_DIR}/rustfs_root_compat_relative_consumer_hits.txt"
@@ -2776,6 +2777,19 @@ if [[ -s "$STORE_API_MODULE_PATH_HITS_FILE" ]]; then
   report_failure "legacy ECStore store_api module files must not be restored: $(paste -sd '; ' "$STORE_API_MODULE_PATH_HITS_FILE")"
 fi
 
+(
+  cd "$ROOT_DIR"
+  {
+    [[ -e crates/ecstore/src/store.rs ]] && printf '%s\n' 'crates/ecstore/src/store.rs'
+    [[ -e crates/ecstore/src/set_disk.rs ]] && printf '%s\n' 'crates/ecstore/src/set_disk.rs'
+    true
+  }
+) >"$ECSTORE_ROOT_STORE_SET_DISK_MODULE_HITS_FILE"
+
+if [[ -s "$ECSTORE_ROOT_STORE_SET_DISK_MODULE_HITS_FILE" ]]; then
+  report_failure "ECStore store and set_disk owners must stay in directory modules: $(paste -sd '; ' "$ECSTORE_ROOT_STORE_SET_DISK_MODULE_HITS_FILE")"
+fi
+
 cat >"$ECSTORE_COMPAT_PASSTHROUGH_EXPECTED_FILE" <<'EOF'
 EOF
 sort -o "$ECSTORE_COMPAT_PASSTHROUGH_EXPECTED_FILE" "$ECSTORE_COMPAT_PASSTHROUGH_EXPECTED_FILE"