KTM won the Czech Grand Prix with Brad Binder, while Miguel Oliveira took his Tech3-run RC16 to the top of the rostrum in the Styrian GP in Austria while Espargaro was third.
But the San Marino GP marked the first round in 2020 where the KTM wasn't a threat for the podium, with Espargaro 12 seconds from the win in 10th ahead of Oliveira and Binder.
Following the test on the Tuesday afterwards, KTM took a step forward and Espargaro ran in the podium battle all race before being passed by Suzuki's Joan Mir and Petronas SRT's Fabio Quartararo late on – though a penalty for the latter promoted the KTM to third.
Espargaro called the leap forward KTM made between the two Misano races "shocking".
"This podium for us is [worth] more than a victory in Austria, because in Austria everything was good, everything was clear, the bike was performing well in all the sessions, warm-up, race," he said.
"It's not easy to fight against these guys, but when the bike is working so well, you can expect these [podium] results.
"But when you arrive like last weekend 12 seconds from first, and today we arrived four or five seconds to Maverick [Vinales], who's been very fast, and we lost this second just at the end of the race because the tyre was gone, I realise how shocking this result is and how much we needed to the result.
"This was one of the races on the calendar along with Barcelona that we knew we would struggle.
"So, let's face Barcelona in the best of ways and let's see how the championship goes, because after Barcelona we know things can be better for us."
Having run the medium tyre in the San Marino race and suffered from a lot of rear locking, Espargaro opted for the soft option for the second Misano outing – though he admits it was a tough decision owing to the uncertainty of the rubber's durability.
"It's been a difficult and hard decision, because Saturday night I was thinking about what to do and after the warm-up I was not really convinced to use the rear soft," he added.
"But I said to myself, if we repeat the same mistake as last weekend, going again with the medium and maybe it doesn't work again, it would be two times the same mistake [was made]. "So, I said let's use the soft, let's enjoy the first 15 laps of the race and then see what's going on.
"I was performing very good, I was keeping Fabio behind at one second, at one stage I was taking some gap to him.
"But 10 laps from the end, the rear tyre say ciao, ciao. Then I started to struggle a lot in some corners, there was a couple of times I was close to high side on entry and then on the exit I didn't have the speed."