The Emirati picked up two points for his ninth-place finish, his first WRC points since Rally Australia in September 2011, but said he had not been able to push anywhere near his maximum due to not feeling comfortable with the car.
"From a personal perspective I am happy but I know I can do better," the 41 year old said.
"There is a lot that we can do to improve the car and our pace and that is what we will be working on in the time ahead before the next event we compete in."
Set-up issues are Sheikh Khalid's biggest issue and he acknowledged that it was harder to find the car's sweet spot than the Ford that he had previously driven in the WRC between 2007 and 2011.
"It is very difficult in the Citroen to find a set-up where you can really push hard," he said.
"In the Ford there was a small margin of set-up, but with the Citroen there are a number of things that can be changed and all of them can change the entire feeling of the car and the set-up.
"It is not easy but I am enjoying working with the team to find the answers we need to improve our pace. I am happy and like challenges and this is one."
Sheikh Khalid, who is the chairman of Abu Dhabi Racing, will miss the next WRC round in Argentina, which takes place between May 3-5, as he instead concentrates on the third round of the Middle East Rally Championship [MERC] in Jordan, which takes place a week later.
He is second in the standings behind Nasser Al Attiyah after finishing runner-up to the Qatari in the opening rounds, and his challenges with getting the Citroen to his satisfaction have made him realistic on his chances of winning his first title since 2004.
"Citroen are new to this terrain and we cannot just expect to get a car right immediately in the championship," he said.
"It is going to take time, maybe two to three years, so hopefully we have time to make this project work and get the car set up well so we can really attack."
Looking back to last weekend's action in Portugal, Sheikh Khalid had vowed in his second WRC event of the season after Sweden in February, to take a cautious approach to the event, and he acknowledged that he had kept to the strategy.
"It was difficult to find a pace that I was comfortable with as I said so I chose not to take risks," he added.
"The important thing was to finish and get the result we could, and I feel we did what we could under difficult circumstances so we have to be happy with that."
While he made up a place on the final leg of the event on Sunday as he went past Esapekka Lappi's Skoda, he missed out on a possible eighth place as he was beaten by Mads Ostberg, the Norwegian driver, who took more than two minutes out of him on the final stage, which had bonus points on offer for the fastest time.
Ostberg, who had led on the first day before crashing, had recovered in his M-Sport Ford and set the second fastest stage time overall to get two extra points on his way to overhauling Sheikh Khalid.
There was no regrets from Sheikh Khalid though, as he added: "I was following Mads on that power stage and his lines were all over the place when I was going through. He was really pushing.
"He knows his Ford very well and he wanted the powerstage points too and really had nothing to lose from where he was. Finishing was important to us and we wanted the points we had so I was happy with what we did under the circumstances we were in."