The JNA's initial orders were to relieve Croatian siege of their barracks in the city and isolate the region of Dalmatia from the rest of Croatia.

JNA bombarded Šibenik, causing damage to numerous structures, including the Cathedral of St. James, a UNESCO World Heritage Site.

The Yugoslav People's Army (Jugoslovenska Narodna Armija – JNA) confiscated Croatia's Territorial Defence weapons to minimise resistance.

Milošević, preferring a campaign to expand Serbia rather than preservation of Yugoslavia, publicly threatened to replace the JNA with a Serbian army and declared that he no longer recognised the authority of the federal Presidency.

Nonetheless, the increasing intensity of the conflict in the region and elsewhere in Croatia led to the preparation of bomb shelters in Zadar by city officials.

[13] Serbian Autonomous Oblast of Krajina (SAO Krajina) authorities called up three Territorial Defence units in the Zadar hinterland on 11 July, one day after another fatal shooting of a Croatian police patrol in the Zadar area,[14] while the JNA 9th (Knin) Corps conscripted the local Serb population in Benkovac to strengthen its ranks by the end of the month.

[15] In late July, a paramilitary group, led by Miro Barešić and formally subordinated to the Croatian Ministry of Defence, conducted several sabotages in the Benkovac area.

[17] On 26 August, the JNA 9th (Knin) Corps openly sided with the SAO Krajina forces as they jointly attacked Kijevo, expelling all Croats from the village.

[20] On 14 September, the ZNG and the Croatian police blockaded and cut utilities to all JNA facilities located in Croatian-controlled territory, beginning the Battle of the Barracks.

[21] The move blockaded 33 large JNA garrisons in Croatia[22] and numerous smaller facilities, including border posts, weapons and ammunition storage depots.

[20] The JNA's planned campaign included an advance in the Šibenik area by the 9th (Knin) Corps, which was tasked with isolating Dalmatia from the rest of Croatia.

[31] The JNA garrison in Šibenik barracks included the 11th Marine Infantry Brigade—one of a handful of units regularly maintained at full combat readiness.

[36] The 600-strong 4th Battalion of the 4th Guards Brigade represented the strongest ZNG unit in the area, while the JNA is estimated by Croatian sources to have deployed approximately 1,500 troops against Drniš.

[39] On the left flank, the JNA advanced towards Drniš, capturing the villages of Maljkovo and Kričke, and interdicting the Drniš–Split, east of the Krka River.

[24] By 17 September, the commanding officer of the JNA 9th (Knin) Corps, Major General Vladimir Vuković, modified the initial deployment plan, because of strong resistance offered by the ZNG and the Croatian police, relying on populated areas and terrain features to hold back the JNA forces north of Vodice.

[27] On the night of 17/18 September, the JNA was ordered to trap and destroy the ZNG force in Drniš and the Miljevci Plateau area, while holding positions achieved elsewhere.

[39] In the morning, the JNA resumed its offensive towards Vodice, on the right flank of the attack,[30] while the ZNG abandoned Drniš and pulled back to the village of Unešić.

[34] On 19 September, the ZNG captured an 88-millimetre (3.5 in) JNA coastal artillery battery on the Smokvica Island and the "Krušćica" barracks near Rogoznica.

[45] On 22 September, a Croatian counter-attack, supported by recently acquired artillery, pushed back the JNA from the bridge by 10:00,[38] extending the ZNG-controlled bridgehead to the area of Gaćelezi, 9 kilometres (5.6 miles) to the northwest.

[47] On 22 September, the Croatian forces captured the JNA "Kuline" barracks in Šibenik itself along with the 15 Yugoslav Navy vessels based there.

The footage, ending in shouts claiming that both of the planes were downed, became one of the most significant pieces of material in terms of propaganda and morale in Croatia.

There are two documentary films covering Šibenik and its surroundings during the battle: My city will be happy too (I moj će grad biti sretan) by Matea Šarić and September War 1991, Šibenik–Vodice (Rujanski rat 1991.