The Briton was omitted from Sky's Tour line-up for the first time since 2014
However, he was not feeling the same force when towing Froome and the team through the French countryside.
“I expected to be going well but I’m creeping to be honest,” he told Cycling Weekly after the stage four Critérium du Dauphiné time trial two weeks ago.
“I’m not really sure why. I really struggled the last few days and then today I haven’t gone anywhere.”
After the Classics, he came back to racing in the Tour of Yorkshire and built up to the Tour, including an altitude camp in Tenerife for a couple of weeks.
The 30-year-old struggled more so since he could not pin-point the problem.
“I’m not medically ill I’ve not got a cold or anything. Sometimes I struggle when I come back down from altitude and the first day of the Dauphiné has been difficult in the past but not to this kind of level…
“Whether I’m on the way down with something that we can’t pick up yet or not, I don’t know.”
Stannard pulled out of the Critérium du Dauphiné ahead of stage five, but appeared back on track when he raced the Route du Sud with Thomas last week.
Sky, however, have plenty of men to select from to fill the mountain domestique spots and flat-land helper spots.
Team boss David Brailsford and head Tour sports director Nicolas Portal would have looked over their options through the Dauphiné, the Tour de Suisse and the Route du Sud.
They had four heavy-lifters with German Christian Knees – keen to race with the Tour starting in Germany – Belarusian Vasil Kiryienka, Welshman Luke Rowe and of course, Stannard.
Brailsford and Portal had to overlook Stannard and mountain helper Wout Poels, who has been battling with a knee injury.
“He’s a good mate of mine, it’s disappointing to see him miss out. Wout too, but Wout is coming back from injury,” Geraint Thomas told Cycling Weekly after the squad announcement on Thursday.
“Ian was always hoping he’d get there, but it’s one of those things. Everyone is so strong, so nothing’s a guarantee.
“It’s sad, but at the same time they will have a lot of other opportunities to go for themselves, whether they do the Vuelta or whatever.
Froome will be supported by Geraint Thomas, Sergio Henao, Mikel Landa, Mikel Nieve, Michal Kwiatkowski, Vasil Kiryienka, Christian Knees and Luke Rowe.
“It’s a definitely a bit of a different feel in the team this year,” Thomas added.
“Still, everyone one apart from Kwiatkowski has been part of our winning teams. Everyone knows what they are doing.”The Tour de France begins on July 1 with a 14km individual time trial through the streets of Düsseldorf.