McGlynn, of Crookston, Glasgow, clinched the first medal of the day, taking a silver in the women's blind and visually impaired tandem time-trial.
The cyclist, 39, who was born with an eye defect, missed first place by just half a second with gold medals later seized by Hannah Cockroft, 20, who triumphed in the T34 100m race with a Paralympic record of 18.05 seconds, and Welsh cyclist Mark Colbourne.
McGlynn, and her pilot Helen Scott, had the fastest time as the penultimate pair in the blind and visually impaired tandem one-kilometre time-trial at the Velodrome.
But world champions Felicity Johnson and Stephanie Morton from Australia agonisingly overhauled them in the final run to grab the gold.
McGlynn said: "I'm a wee bit disappointed but we came into it really well prepared and thought we had it, but that's bike racing. It doesn't always happen the way you wanted it to.
"I've definitely got more to offer. In training we're the fastest starters and there's more to come. It just didn't work out for us this time.
"It's been amazing – to have all the support from the crowd here and back home has been fantastic and I can't thank everyone enough.
"Paralympic sport is moving on and the Australians have beaten us three times now, so they've set a high benchmark. But we definitely have the potential to beat them."
She said she was desperate to compete in the next games in 2016, adding: "It all depends on what the team management thinks and whether I'm getting past it or not. But I would definitely like to continue to Rio."
McGlynn previously won gold in Athens and Beijing but finished behind the Australians with new partner Scott, from Halesowen in the West Midlands, at the World Championships in Los Angeles earlier this year.
Lorna Turnham, piloted by Aberdeen police officer Fiona Duncan, yesterday finished just out of the medals in fourth.
Britain's medal haul on day two of the Paralympics included two golds, seven silver and three bronze.
Mark Colbourne claimed Paralympic gold for the first time at the London 2012 velodrome after winning Britain's first medal of the games on Thursday. He won the men's C1 three-kilometres individual pursuit in a world record of three minutes 53.881 seconds.
Jon-Allan Butterworth won silver in the velodrome in the men's individual time trial C4-5, but GB favourite Jody Cundy's bid to secure gold ended in controversy and anger as officials denied him a restart.
There was silver and bronze for Britain in the men's C3 individual pursuit.
Meanwhile, activists staged a protest at the Department for Work and Pensions (DWP) against multinational IT firm and Paralympics sponsor Atos, which carries out the Government's "fit for work" assessments.
Disabled and anti-cuts campaigners have been rallying all over the country for the last week because they claim the tests by Atos are "damaging and distressing".
Yesterday they took their protest to Atos's London headquarters before carrying out a "secret action" at the DWP's building in central London.
Several protesters got into the building and a further two in wheelchairs chained themselves to the doors, according to UK Uncut who have been staging the protests with Disabled People Against Cuts.