The Scots endured a difficult start to the campaign, including a 2-0 defeat in Brussels the last time the two nations met, a match which proved to be Craig Levein's last in charge.
The national team appears to be back on track under Gordon Strachan and earned a shock first group win in Croatia in June, before producing a decent display against England in a friendly at Wembley last month.
Belgium sit three points clear at the top of Group A and while Scotland's own hopes of qualification are long gone, Wilmots insists he is taking nothing for granted.
He said: "We will suffer tomorrow [Friday], that's for sure.
"Scotland are not that bad because they played two very good games against very good opponents, Croatia and England.
"They had a bad start to the group but now they are back."
He added: "They are in a winning spirit, in a good spirit.
"They are playing at home. They are already eliminated and they can play more relaxed, more free.
"They have a new coach and they had a great result against Croatia and a good game against England, where they were leading twice.
"They are in a good spirit to start this game."
Wilmots revealed he is sweating over the fitness of four key players, with Jan Vertonghen, Eden Hazard, Nacer Chadli and Axel Witsel all injury doubts.
The coach said: "We will see tomorrow [Friday] who is fit and who is not and we will make the decision we have to make.
"We will do everything to win tomorrow [Friday] with no fear. Everyone who plays will be ready and focused on the game."
Like Wilmots, Vertonghen fully expects Scotland to be a different prospect to the side they met last October.
He said: "It will be a very hard game for us. We played them at home and they were very difficult to beat.
"At Hampden, it will be even more difficult. We will have to be at the top of our game. They did well against Croatia and England.
"I think we will see another Scotland tomorrow [Friday]. They looked very confident in their last two games.
"Everybody has to be at 100 per cent to beat Scotland at Hampden."
The Tottenham defender hopes the meeting with Scotland will provide another step towards achieving his aim of playing at the World Cup finals.
He said: "It would be one of the highlights of my career. That's what everybody wants as a football player.
"It would be a great achievement. It's one of the goals of my career and I hope I can achieve it in this campaign."