The 50-year-old Argentine has arrived at the Nou Camp as a disciple of the Catalan club's trademark possession game and has said all he wants to tweak is to recover the high-intensity pressuring of rivals in the attacking third.
Other smaller changes to their system were evident in Sunday's La Liga opening 7-0 home rout of Levante, however, especially with his handling of World Player of the Year Messi, midfielder Cesc Fabregas and new signing Neymar.
Messi was taken off without being injured after 70 minutes, but with the scoreline at 6-0, something almost unheard of in the Pep Guardiola and Tito Vilanova eras.
He was last substituted uninjured in 2010.
"I had already spoken to Messi about it. The season is very long with many games and he is intelligent and understands it is necessary," Martino said.
"In an evenly-balanced match no one would take him off...but it is important to look after him and safeguard his fitness."
The hammering of a weak Levante side offered up few pointers as to how Martino's side is really shaping up, but a trip to play Atletico Madrid in Wednesday's Spanish Super Cup first leg should be more revealing.
While tiny Levante are a side who have overhauled their squad on a shoestring budget, Atletico have a settled team who finished third in La Liga last year and beat Real Madrid 2-1 at the Bernabeu in the King's Cup final in May.
Diego Simeone's side were 3-1 winners at Sevilla in their opening game on Sunday.
Messi will surely start but Martino's other choices should be more intriguing.
Neither Guardiola nor Vilanova successfully resolved how to integrate the talents of Fabregas, who was outstanding against Levante, into the side on a regular basis.
Martino started with Fabregas in midfield and moved him into Messi's position up front when the Argentine was substituted, bringing Andres Iniesta off the bench - the type of common sense rotation that could prove fruitful across the season.
In an attempt to keep the pressure off new 57 million euros (£48 million) signing Neymar, the 21-year-old Brazil forward was only brought on for the last half hour as he continues to find his feet in Spain.
"There is no rush," Martino said. "He needs a little more time."
Atletico's victory against Sevilla, direct rivals for the Champions League places, saw Simeone being asked if the club were ready to challenge the top two in the league.
"Absolutely not," the Argentine said on Sunday.
"Madrid and Barca play in a different league. This is a boring championship. We will have to wait until there is a more equal division of television revenues, because for the time being it is only a two-team title race."
Real and Barca scoop up almost half of all the cash La Liga generates in TV revenues with individually negotiated deals - a hot topic in Spain as the other 18 top-flight clubs press for a more equitable, collectively bargained arrangement.
For this reason, the Spanish Super Cup appears a more succulent opportunity for silverware for Atletico than Barca.
Atletico are all too aware that a title bid or a Champions League final are distant dreams, but the King's Cup and the season-opening Super Cup are far more attainable against bigger clubs distracted by the main prizes.
After their Europa League triumphs in 2010 and 2012, Atletico were far more up for the ensuing European Super Cups than either of their Champions League-winning adversaries Inter Milan or Chelsea.
Inter were beaten 2-0 and Chelsea trounced 4-1 and the only difference with the Spanish Super Cup is that it is over two legs and Barca are far more aware of what Atletico are all about.
- Sports & Recreation
- La Liga
- Cesc Fabregas
- Atletico Madrid
- Pep Guardiola