diff --git a/src/Types.jl b/src/Types.jl
index 7651d9ece5..ebd221d060 100644
--- a/src/Types.jl
+++ b/src/Types.jl
@@ -463,15 +463,50 @@ function write_env_usage(source_file::AbstractString, usage_filepath::AbstractSt
     # Ensure that log dir exists
     !ispath(logdir()) && mkpath(logdir())
 
-    # Generate entire entry as a string first
-    entry = sprint() do io
-        TOML.print(io, Dict(source_file => [Dict("time" => now())]))
-    end
-
-    # Append entry to log file in one chunk
     usage_file = joinpath(logdir(), usage_filepath)
-    open(usage_file, append=true) do io
-        write(io, entry)
+    timestamp = now()
+
+    ## Atomically write usage file
+    while true
+        # read existing usage file
+        usage = if isfile(usage_file)
+            TOML.parsefile(usage_file)
+        else
+            Dict{String, Any}()
+        end
+
+        # record new usage
+        usage[source_file] = [Dict("time" => timestamp)]
+
+        # keep only latest usage info
+        for k in keys(usage)
+            times = map(d -> Dates.DateTime(d["time"]), usage[k])
+            usage[k] = [Dict("time" => maximum(times))]
+        end
+
+        # Write to a temp file in the same directory as the destination
+        temp_usage_file = tempname(logdir())
+        open(temp_usage_file, "w") do io
+            TOML.print(io, usage, sorted=true)
+        end
+
+        # Move the temp file into place, replacing the original
+        mv(temp_usage_file, usage_file, force = true)
+
+        # Check that the new file has what we want in it
+        new_usage = if isfile(usage_file)
+            TOML.parsefile(usage_file)
+        else
+            Dict{String, Any}()
+        end
+        if haskey(new_usage, source_file)
+            for e in new_usage[source_file]
+                if Dates.DateTime(e["time"]) >= timestamp
+                    return
+                end
+            end
+        end
+        # If not, try again
     end
 end