Mr MacNeil’s closest political ally, Inverclyde councillor Chris McEleny, made the jump when the party was launched last week and will now stand on the party’s West Scotland list.
Both Mr MacNeil and Mr McEleny have pushed for a “plan B” for Scottish independence from within the SNP, but to no avail.
With speculation rife about his possible departure from the party, Mr MacNeil told The National leaving the SNP was never a thought in his mind.
“I had no intention of joining, it was never something I intended to do,” he said.
“I can’t say that I am unhappy that there is a change in the dial on the focus on independence in this election.”
There have already been a number of high-profile defections from the SNP to Alba, including current SNP MPs Kenny MacAskill and Neale Hanvey, as well as Mr McEleny and former MP George Kerevan.
Upon Mr MacAskill’s departure, he was branded an “embarrassment” by SNP Westminster leader Ian Blackford, who described the defection as a “relief”.
But Western Isles MP Mr MacNeil said he would not encourage such backbiting between the two parties.
“The more parties of independence the better, eventually of course all parties will be parties of independence – same story in every country,” he said.
“Also I won’t be encouraging snide or smearing remarks about the Alba Party. We should instead be arguing against those trying to block independence, not denigrate those who are for it, and keeping the discourse positive.”
He added: “It makes the Scottish election very interesting indeed. Anybody who thinks independence is important will be pleased there are now two serious parties of independence rather than one.”
Despite the tactical voting pitch from Alba, which is calling for independence supporters to give them their votes on the regional list to create a “supermajority” for independence, Mr MacNeil said he planned to give both of his votes to the SNP.
He told the paper: “I can see the argument people have when they use calculators and logic.”