diff --git a/master_changes.md b/master_changes.md
index 9c4975018f5..95a0f4860ed 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -75,6 +75,7 @@ users)
 ## Env
 
 ## Opamfile
+  * Make all writes atomic [#5489 @kit-ty-kate]
 
 ## External dependencies
  * Always pass --no-version-check and --no-write-registry to Cygwin setup [#6046 @dra27]
diff --git a/src/core/opamFilename.ml b/src/core/opamFilename.ml
index d925d439179..27c5dbf59bf 100644
--- a/src/core/opamFilename.ml
+++ b/src/core/opamFilename.ml
@@ -232,7 +232,7 @@ let with_open_out_bin_aux open_out_bin filename f =
     OpamStd.Exn.finalise e @@ fun () ->
     close_out oc; remove filename
 
-let with_open_out_bin =
+let with_open_out_bin [@deprecated] =
   with_open_out_bin_aux (fun f -> (), open_out_bin f)
 
 let with_open_out_bin_atomic filename f =
diff --git a/src/core/opamFilename.mli b/src/core/opamFilename.mli
index 6a67d5b1695..44b9e3a467c 100644
--- a/src/core/opamFilename.mli
+++ b/src/core/opamFilename.mli
@@ -147,9 +147,11 @@ val open_out_bin: t -> out_channel
     If [f] raises an exception, then [filename] is deleted and then exception is
     propagated. The out_channel does not have to be closed by [f]. *)
 val with_open_out_bin: t -> (out_channel -> unit) -> unit
+[@@deprecated "use with_open_out_bin_atomic instead"]
 
-(** As {!with_open_out_bin} except that the file is written atomically. If [f]
-    raises an exception, then [filename] will be unaltered. *)
+(** [with_open_out_bin_atomic filename f] opens [f] and passes the out_channel to [f].
+    If [f] raises an exception, then [filename] will be unaltered and then exception is
+    propagated. The out_channel does not have to be closed by [f]. *)
 val with_open_out_bin_atomic: t -> (out_channel -> unit) -> unit
 
 (** Removes everything in [filename] if existed. *)
diff --git a/src/format/opamFile.ml b/src/format/opamFile.ml
index b8da4ae8108..eb1d104b699 100644
--- a/src/format/opamFile.ml
+++ b/src/format/opamFile.ml
@@ -76,7 +76,6 @@ end
 
 module type IO_Arg = sig
   val internal : string
-  val atomic : bool
   type t
   val empty : t
   val of_channel : 'a typed_file -> in_channel  -> t
@@ -110,15 +109,10 @@ module MakeIO (F : IO_Arg) = struct
   let write f v =
     let filename = OpamFilename.to_string f in
     let chrono = OpamConsole.timer () in
-    let write =
-      if F.atomic then
-        OpamFilename.with_open_out_bin_atomic
-      else
-        OpamFilename.with_open_out_bin
-    in
+    let write = OpamFilename.with_open_out_bin_atomic in
     write f (fun oc -> F.to_channel f oc v);
     Stats.write_files := filename :: !Stats.write_files;
-    log "Wrote %s%s in %.3fs" filename (if F.atomic then " atomically" else "") (chrono ())
+    log "Wrote %s atomically in %.3fs" filename (chrono ())
 
   let read_opt f =
     let filename = OpamFilename.prettify f in
@@ -195,7 +189,6 @@ end
 module DescrIO = struct
 
   let internal = "descr"
-  let atomic = false
   let format_version = OpamVersion.of_string "0"
 
   type t = string * string
@@ -288,8 +281,6 @@ module LinesBase = struct
 
   let internal = "lines"
 
-  let atomic = false
-
   let find_escapes s len =
     let rec aux acc i =
       if i < 0 then acc else
@@ -379,7 +370,6 @@ end
 
 module type LineFileArg = sig
   val internal: string
-  val atomic: bool
   type t
   val empty: t
   val pp: (string list list, t) Pp.t
@@ -416,7 +406,6 @@ end
 module Aliases = LineFile(struct
 
     let internal = "aliases"
-    let atomic = false
 
     type t = string switch_map
 
@@ -435,7 +424,6 @@ module Aliases = LineFile(struct
 module Repo_index (A : OpamStd.ABSTRACT) = LineFile(struct
 
     let internal = "repo-index"
-    let atomic = false
 
     type t = (repository_name * string option) A.Map.t
 
@@ -457,7 +445,6 @@ module Package_index = Repo_index(OpamPackage)
 module PkgList = LineFile (struct
 
     let internal = "package-version-list"
-    let atomic = false
 
     type t = package_set
 
@@ -528,7 +515,6 @@ module Pinned_legacy = struct
   include LineFile(struct
 
       let internal = "pinned"
-      let atomic = false
 
       type t = pin_option OpamPackage.Name.Map.t
 
@@ -553,7 +539,6 @@ external open_env_updates:
 module Environment = struct include LineFile(struct
 
     let internal = "environment"
-    let atomic = true
 
     type t = (spf_resolved, euok_writeable) env_update list
 
@@ -729,7 +714,6 @@ end
 module File_attributes = LineFile(struct
 
     let internal = "file_attributes"
-    let atomic = false
 
     type t = file_attribute_set
 
@@ -756,7 +740,6 @@ module File_attributes = LineFile(struct
 module StateTable = struct
 
   let internal = "export"
-  let atomic = false
 
   module M = OpamPackage.Name.Map
 
@@ -1174,7 +1157,6 @@ end
 
 module type SyntaxFileArg = sig
   val internal: string
-  val atomic: bool
   val format_version: OpamVersion.t
   type t
   val empty: t
@@ -1215,7 +1197,6 @@ module SyntaxFile(X: SyntaxFileArg) : IO_FILE with type t := X.t = struct
   include MakeIO(struct
       include X
       include IO
-      let atomic = false
     end)
 
 end
@@ -1392,7 +1373,6 @@ end
 module ConfigSyntax = struct
 
   let internal = "config"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.1"
   let file_format_version = OpamVersion.of_string "2.0"
   let root_version = OpamVersion.of_string "2.2"
@@ -1711,7 +1691,6 @@ end
 
 module InitConfigSyntax = struct
   let internal = "init-config"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   type t = {
@@ -1972,7 +1951,6 @@ end
 module Repos_configSyntax = struct
 
   let internal = "repos-config"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
   let file_format_version = OpamVersion.of_string "2.0"
 
@@ -2017,7 +1995,6 @@ end
 module Switch_configSyntax = struct
 
   let internal = "switch-config"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.1"
   let file_format_version = OpamVersion.of_string "2.0"
   let oldest_compatible_format_version = OpamVersion.of_string "2.0"
@@ -2134,7 +2111,6 @@ end
 module SwitchSelectionsSyntax = struct
 
   let internal = "switch-state"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
   let file_format_version = OpamVersion.of_string "2.0"
 
@@ -2205,7 +2181,6 @@ end
 module Repo_config_legacySyntax = struct
 
   let internal = "repo-file"
-  let atomic = false
   let format_version = OpamVersion.of_string "1.2"
 
   type t = {
@@ -2270,7 +2245,6 @@ end
 module Dot_configSyntax = struct
 
   let internal = ".config"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   type t = {
@@ -2363,7 +2337,6 @@ end
 module RepoSyntax = struct
 
   let internal = "repo"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   type t = {
@@ -2453,7 +2426,6 @@ end
 module URLSyntax = struct
 
   let internal = "url-file"
-  let atomic = false
   let format_version = OpamVersion.of_string "1.2"
 
   type t = {
@@ -2567,7 +2539,6 @@ end
 module OPAMSyntax = struct
 
   let internal = "opam"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   type t = {
@@ -3709,7 +3680,6 @@ end
 module Dot_installSyntax = struct
 
   let internal = ".install"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   type t =  {
@@ -3877,7 +3847,6 @@ end
 
 module ChangesSyntax = struct
   let internal = "changes"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.0"
 
   open OpamDirTrack
@@ -3943,7 +3912,6 @@ end
 module SwitchExportSyntax = struct
 
   let internal = "switch-export"
-  let atomic = false
   let format_version = OpamVersion.of_string "2.1"
 
   type t = {
@@ -4021,7 +3989,6 @@ end
 module CompSyntax = struct
 
   let internal = "comp"
-  let atomic = false
   let format_version = OpamVersion.of_string "1.2"
 
   type compiler = string
diff --git a/src/format/opamFile.mli b/src/format/opamFile.mli
index 3274789cbce..00d529c84a8 100644
--- a/src/format/opamFile.mli
+++ b/src/format/opamFile.mli
@@ -1162,7 +1162,6 @@ end
 
 module type SyntaxFileArg = sig
   val internal: string
-  val atomic: bool
   val format_version: OpamVersion.t
   type t
   val empty: t
@@ -1173,7 +1172,6 @@ module SyntaxFile(X: SyntaxFileArg) : IO_FILE with type t := X.t
 
 module type LineFileArg = sig
   val internal: string
-  val atomic: bool
   type t
   val empty: t
   val pp: (string list list, t) OpamPp.t
diff --git a/tests/reftests/dot-install.test b/tests/reftests/dot-install.test
index 18bd526b836..0d70b16509d 100644
--- a/tests/reftests/dot-install.test
+++ b/tests/reftests/dot-install.test
@@ -211,7 +211,7 @@ Not found: ${BASEDIR}/OPAM/inst/.opam-switch/install/dot.changes
   - install lot-of-files ~dev
 SYSTEM                          mkdir ${BASEDIR}/OPAM/inst/.opam-switch/build/lot-of-files.~dev
 SYSTEM                          copy ${BASEDIR}/OPAM/repo/default/packages/lot-of-files/lot-of-files.~dev/files/lot-of-files.install.in -> ${BASEDIR}/OPAM/inst/.opam-switch/build/lot-of-files.~dev/lot-of-files.install.in
-FILE(.config)                   Wrote ${BASEDIR}/OPAM/inst/.opam-switch/config/lot-of-files.config in 0.000s
+FILE(.config)                   Wrote ${BASEDIR}/OPAM/inst/.opam-switch/config/lot-of-files.config atomically in 0.000s
 SYSTEM                          install ${BASEDIR}/OPAM/inst/.opam-switch/build/lot-of-files.~dev/fichier -> ${BASEDIR}/OPAM/inst/bin/fichier (755)
 SYSTEM                          mkdir ${BASEDIR}/OPAM/inst/lib/lot-of-files
 SYSTEM                          install ${BASEDIR}/OPAM/inst/.opam-switch/build/lot-of-files.~dev/a-file -> ${BASEDIR}/OPAM/inst/lib/lot-of-files/a-file (644)
diff --git a/tests/reftests/opamroot-versions.test b/tests/reftests/opamroot-versions.test
index 834a0d95b38..4caf6a95c87 100644
--- a/tests/reftests/opamroot-versions.test
+++ b/tests/reftests/opamroot-versions.test
@@ -1244,7 +1244,7 @@ Update done, please now retry your command.
 # Return code 10 #
 ### # ro global state, ro repo state, rw switch state
 ### opam install i-am-package
-FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config in 0.000s
+FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config atomically in 0.000s
 GSTATE                          LOAD-GLOBAL-STATE @ ${BASEDIR}/OPAM
 RSTATE                          LOAD-REPOSITORY-STATE @ ${BASEDIR}/OPAM
 RSTATE                          Cache found
@@ -1297,7 +1297,7 @@ roots: ["i-am-package.2" "i-am-sys-compiler.2"]
 ### ocaml generate.ml $OPAMROOTVERSION orphaned 2.1~alpha
 ### # ro global state, ro repo state, ro switch state
 ### opam list
-FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config in 0.000s
+FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config atomically in 0.000s
 GSTATE                          LOAD-GLOBAL-STATE @ ${BASEDIR}/OPAM
 RSTATE                          LOAD-REPOSITORY-STATE @ ${BASEDIR}/OPAM
 RSTATE                          No cache found
@@ -1616,7 +1616,7 @@ Update done, please now retry your command.
 # Return code 10 #
 ### # ro global state, ro repo state, rw switch state
 ### opam install i-am-package
-FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config in 0.000s
+FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config atomically in 0.000s
 GSTATE                          LOAD-GLOBAL-STATE @ ${BASEDIR}/OPAM
 RSTATE                          LOAD-REPOSITORY-STATE @ ${BASEDIR}/OPAM
 RSTATE                          Cache found
@@ -1669,7 +1669,7 @@ roots: ["i-am-package.2" "i-am-sys-compiler.2"]
 ### ocaml generate.ml $OPAMROOTVERSION orphaned 2.1~alpha2
 ### # ro global state, ro repo state, ro switch state
 ### opam list
-FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config in 0.000s
+FILE(switch-config)             Wrote ${BASEDIR}/_opam/.opam-switch/switch-config atomically in 0.000s
 GSTATE                          LOAD-GLOBAL-STATE @ ${BASEDIR}/OPAM
 RSTATE                          LOAD-REPOSITORY-STATE @ ${BASEDIR}/OPAM
 RSTATE                          No cache found
diff --git a/tests/reftests/repository.test b/tests/reftests/repository.test
index 95a7dafb775..94abd2b1bd8 100644
--- a/tests/reftests/repository.test
+++ b/tests/reftests/repository.test
@@ -122,7 +122,7 @@ FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/fo
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.2/opam in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.1/opam in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.5/opam in 0.000s
-FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config in 0.000s
+FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config atomically in 0.000s
 CACHE(repository)               Writing the repository cache to ${BASEDIR}/OPAM/repo/state-hash.cache ...
 CACHE(repository)               ${BASEDIR}/OPAM/repo/state-hash.cache written in 0.000s
 Now run 'opam upgrade' to apply any package updates.
@@ -203,7 +203,7 @@ FILE(repo)                      Read ${BASEDIR}/OPAM/repo/repo2/repo in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/repo2/packages/bar/bar.2/opam in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/repo2/packages/bar/bar.1/opam in 0.000s
 [tarred] no changes from file://${BASEDIR}/REPO
-FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config in 0.000s
+FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config atomically in 0.000s
 CACHE(repository)               Writing the repository cache to ${BASEDIR}/OPAM/repo/state-hash.cache ...
 CACHE(repository)               ${BASEDIR}/OPAM/repo/state-hash.cache written in 0.000s
 Now run 'opam upgrade' to apply any package updates.
@@ -247,7 +247,7 @@ FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/fo
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.2/opam in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.1/opam in 0.000s
 FILE(opam)                      Read ${BASEDIR}/OPAM/repo/tarred/packages/foo/foo.5/opam in 0.000s
-FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config in 0.000s
+FILE(repos-config)              Wrote ${BASEDIR}/OPAM/repo/repos-config atomically in 0.000s
 CACHE(repository)               Writing the repository cache to ${BASEDIR}/OPAM/repo/state-hash.cache ...
 CACHE(repository)               ${BASEDIR}/OPAM/repo/state-hash.cache written in 0.000s
 Now run 'opam upgrade' to apply any package updates.