Upon Alexander's return, both Olympias and Philip began to express concern about the boy's lack of heterosexual interest. Reared by his mother, Alexander did indeed show effeminate qualities. His parents even went so far as to find a potential partner with whom they encouraged Alexander to have intercourse.

While his sexual masculinity may have been slow in developing, Alexander immediately showed his prowess on the battlefield. Philip had not been long departed when a rebellion arose among the Maedi, the fierce and powerful tribe that dwelled in Thrace. Alexander went himself to subdue the rebels, and he turned their city into a military outpost for Macedonia, which was renamed Alexandropolis–in imitation of Philippopolis, founded by the king two years before. Although Philip continued to treat Alexander as a protégé, it became evident before long that the latter was competing with–if not challenging–the former's authority.

Meanwhile, Philip's campaign was going poorly, and the position of Macedonia becoming more vulnerable. His worst fears were realized when Athens and Thebes, longtime rivals, formed a coalition against Macedonia. Philip handled the ensuing conflicts expertly. In the decisive battle at Chaeronea, Alexander took command of the left wing, facing the Thebans, while Philip maintained the traditional post of the king at the right of the army, facing the Athenians. Alexander's responsibility was great, for it was on the Thebans–better trained and with more to lose than the Athenians, for they technically had been Macedonian allies–that victory or defeat depended. Alexander also had to face the famed Sacred Band, which in 371 B.C. had led the victory over the previously invincible Spartan army.

Alexander's own victory was secured, ironically, because of the superior discipline of the Sacred Band. When they held their position and the other troops did not, Alexander was able to swoop into the gap and soon had the Theban army surrounded. The rest of the troops were handled effectively, and all that remained were the 300 Thebans of the Sacred Band who fought valiantly to their deaths. Only forty-six were taken alive, while the remaining 254 were buried on site, where they lie to this day in a famous common grave.

Philip recognized that his victory over Athens did not give him license to rule tyrannically, as the situation remained precarious. He therefore offered terms so generous that Athens accepted without argument or much time to reconsider. On the other hand, the powers of Thebes had to be dismantled systematically. Its leaders had already betrayed Macedonia once, so they could no longer be trusted. Moreover, as Thebes did not have the fleet that made Athens more intimidating, Philip chose to act severely while he could.

With these powers defeated, Macedonia became the undisputed leader of the Greek city-states. Philip used this influence to form the Hellenic League, which he designed not only to maintain peace among the Greek states but to join him in the invasion of the Persian empire. Only Sparta refused to participate. Not itself a league member, Macedonia formed a separate alliance with S[arta, and Philip served as its leader, or Hegemon. Still, leaders of the other states harbored resentment toward Macedonia, which they still viewed as no more than a semi-barbaric nation that had won its right to rule through force. This unstable loyalty was a problem that neither Philip nor Alexander would ever fully overcome.

During this time of political conflict, Philip also had to face domestic problems. Although Alexander's war heroics had won him the favor of many Macedonians, some members of the nobility expressed disapproval. In particular, they disliked Olympias and feared the devotion Alexander displayed toward her. Moreover, they was noted that Alexander had shown traces of arrogance, whereas his father had been more liable to treat his subjects as peers. With all of this trouble already brewing, Philip further complicated matters by making the controversial move of marrying Cleopatra, the niece of Attalus, a strong enemy of Alexander. Moreover, Philip divorced Olympias on the grounds of suspected adultery, and he encouraged rumors that Alexander himself may have been illegitimate. The implications were clear: Philip was paving the way for a new successor.

At the wedding feast, at which all parties were heavily intoxicated, Attalus rose to propose a toast, and in doing so he expressed the hope that a legitimate successor to the kingdom might be born to Philip and Cleopatra. This public provocation infuriated Alexander, who flung his goblet in Attalus's face and challenged, "Are you calling me a bastard?" Philip jumped to his feet, drew his sword, and started toward Alexander, only to fall flat on his face. Alexander is said to have mocked, "That, gentlemen, is the man who's been preparing to cross from Europe into Asia–and he can't even make it from one couch to the next!" Alexander then exited quickly, and the next morning he was escorting his mother to her native home in Epirus.