Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl-L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway. malonyl-[ACP] + S-adenosyl-L-methionine = malonyl-[ACP] methyl ester + S-adenosyl-L-homocysteine Cofactor biosynthesis; biotin biosynthesis. Belongs to the methyltransferase superfamily.