Santana began throwing off the mound at the Mets' Spring Training complex in Port St. Lucie, Fla., in late May.
Though the southpaw experienced soreness in his left shoulder during a rehab assignment on June 3, he never stopped throwing.
Instead of throwing off a mound, Santana played catch and long-tossed, and pushed back his next scheduled bullpen session.
"What happened in that situation was we had scheduled to throw a couple of times in a week, and then I just felt like ... it wasn't a good day for me to get on the mound," Santana said. "That was the end of it. My body was telling me to long-toss more than just get on the mound because that intensity was different than what I was doing."
The 32-year-old left-hander believes that actually helped in his recovery process.
"The key here is to make sure you understand and listen to your body more than anything," Santana said. "Just because you have a program written down doesn't mean you have to follow it exactly how it is."
Whether Santana throws another light BP or a minor league game next depends on how he feels following his session on Sunday.
On Friday, Santana threw over 40 pitches that totaled three innings as part of a simulated game. His focus over the past few weeks has been building up his strength.
One thing the three-time All-Star hasn't paid attention to is his velocity because he considers it "too early" to think about how fast he's pitching. What matters most to him is feeling comfortable throwing all of his pitches.
During his three seasons with the Mets, Santana has also undergone knee and elbow surgery. He is 40-25 with a 2.85 ERA in his 88 starts, including seven complete games.
"I want to pitch right now. I want to be here, but reality is that I can't. This is a long process, and we're taking everything very carefully. If it's my choice I could be here right now but reality is I can't," Santana said.
"I worry about being healthy, that's what I worry about. Pitching this year, that's not what I worry about. Looking towards the future, that's what we want. I'm working my way back, and I hope to be back sometime this season. That's where we're at right now and that's what I want to do. But if that doesn't happen doesn't mean that's the end of the world."