You might be interested in this issue on Github: Support dynamic file naming.

Had the same problem recently, you can also make the change of filename by tweaking the changeset (see https://github.com/elixir-waffle/waffle_ecto/issues/13) However, Waffle automatically added file extension and I gave up with this solution. Using the underlying ExAws.S3 is actually not hard and gives more flexibility if you don’t need advanced Waffle features.

Thanks for your suggestions!
After banging my head against this trying to to find a safe and effective solution i decided to solve the problem outside of waffle. So in my controllers I now have a function that goes through the attachments in the parameters and adjusts the filenames in the different %Plug.Upload{}.

  def unique_attachments(params, options \\ []) do
    defaults = [
      field: "attachments"
    ]

    options = defaults |> Keyword.merge(options) |> Enum.into(%{})

    attachments = Map.get(params, options.field, %{})

    Enum.reduce(attachments, %{}, fn {key, value}, acc ->
      case Map.get(value, "file", nil) do
        nil ->
          Map.put(acc, key, value)

        file ->
          filename = Map.fetch!(file, :filename)
          unique_filename = "#{:os.system_time()}_#{filename}"
          file = Map.put(file, :filename, unique_filename)
          value = Map.put(value, "file", file)
          Map.put(acc, key, value)
      end
    end)
  end

It’s not elegant but it works and it does not risk corrupting my old existing attachments, since it will only apply to new files.