The answer is: Yes, you can!
The Malay language (bahasa Melayu) has a large number of local dialects such as Johor, Minangkabau, Jakarta, Manado or Kelantan Malay. Besides these regional dialects, the Malay language also consists of two major branches, namely Indonesian-Malay known as bahasa Indonesia, and Malaysian-Malay known as bahasa Malaysia (the meaning of bahasa is ‘language’).
There are certain differences between formal bahasa Malaysia and formal bahasa Indonesia, but the languages are very similar. Listening to a speech delivered in formal language, it can take a while before one knows whether the language is Indonesian or Malaysian.
In colloquial speech, the differences are naturally much more pronounced. But even between different regions within Indonesia and within Malaysia there are considerable differences between, let’s say, Jakarta and Kupang Malay (both spoken in Indonesia), or Kelantan and Johor Malay (spoken in Malaysia).
Formal Indonesian and formal Malaysian are thus very similar, and mutually intelligible.
The language that we teach in “The Indonesian Way” is bahasa Indonesia. If you are interested in learning bahasa Malaysia instead of bahasa Indonesia, let us know. It is relatively easy for us to let you know the differences between the two languages. Also: every educated Malaysian is aware of the subtle differences between Malaysian and Indonesian, and will not have any difficulties understanding you even if you speak with a distinct Indonesian accent!
If you want to learn more about the history of the Malay language and the relation between Indonesian and Malaysian, read J. Collin (1998) “Malay, world language: a short history” or the Wikipedia article “History of the Malay language”