But escalating tensions came to a boil last week when pro-STC forces seized all key government and military locations on Socotra island, declared self-administrative authority, and appointed its own acting governor.
The move, though carried out by a small number of fighters with little bloodshed, proved to be a significant turning point in the more than five-year conflict, prompting severe criticism of the Saudi-led coalition by government officials who accused it of "betrayal".
Shortly after, pro-Saudi media was ripe with reports of alleged Turkish-Qatari-Muslim Brotherhood activities in Yemen, noting the takeover had curbed the axis' "growing influence" on the island.
However, Yemen experts and political analysts have dismissed the claims as mere excuses by the coalition designed to sow discord.
"There's no Turkish presence in Socotra. Islah doesn't control the archipelago either. There's no Houthi presence there as well," Yemen and Gulf analyst at the Middle East Institute, Ibrahim Jalal, told The New Arab.
"These are redundant excuses to mask foreign interests. The expelled governor was a young, socialist politician from Socotra itself, where the UAE, among others, has crystal clear strategic interests evident in its April 2018 deployment of heavy arms and troops that further strained Yemeni-Emirati relations," Jalal added.
The infighting has emerged as a second front in a country already split by a five-year war between Houthi rebels, who control the capital Sanaa and the north, and the government, which was forced south to the interim capital of Aden.
The latest developments come just months after the Riyadh Agreement - which was struck last November but quickly became defunct - a power-sharing deal for the south, where a separatist insurgency has revived long-standing independence ambitions.
The STC, backed by the UAE, first declared self-rule on 26 April, accusing the government of failing to carry out its duties, before moving on to Socotra.
The once peaceful island, situated near strategic shipping lanes and famed for its rare and picturesque biodiversity, has long been a weak spot for all parties involved in the conflict, all of which have in recent years attempted to sneak their way into the hearts of the local population.
"Socotra and other regions in South Yemen face deep political divisions," Mohammed Albasha of the US-based Navanti Group told The New Arab.
"Navanti Group's latest polling of public opinion in Socotra tells the story of a divided house between those who support the ROYG and those who support the STC. In principle Socotra's remoteness should have isolated the island from the civil war on the mainland. However, the presence of competing political parties have torn Socotra's social and political fabric," he added.
But the reasons for bypassing Yemen's internationally-recognised government, as well as its sovereignty, have remained vague and a former diplomat who spoke to The New Arab on condition of anonymity blamed it on the lack of leadership.
"The absence of Hadi created a vacuum that has allowed everyone free reign to play, and it signifies the collapse of Hadi's authority even as a symbolic president," the source said. Meanwhile, Jalal believes it to be a strategy to push for stalled agreements.
"The actor that green-lighted the Abyan battle in May to pressure the UAE-backed STC tacitly approved the latter's takeover of Hadibo, Socotra, to pressure the government to renew talks on the stalled Riyadh Agreement," Jalal said, in comments that were recently solidified with an announced de-escalation meeting in Saudi Arabia between members of the bickering allies.
On Monday, the Saudi-led military coalition announced a ceasefire, with coalition spokesman Turki Al-Maliki confirming the allies-turned-rivals would hold fresh talks in Saudi Arabia to discuss the truce.
"The Coalition welcomes the response of the legitimate government of Yemen and the Southern Transitional Council for its request of a comprehensive ceasefire, de-escalation and a meeting to be convened in the kingdom," Maliki said in a statement carried on state media.
He said the process would advance the implementation of the Riyadh Agreement.
Just days later, the coalition said it had deployed observers to monitor the ceasefire between pro-government troops and southern separatists, as military sources said fresh clashes had broken out.
Saudi forces arrived on Wednesday in Shaqra and Sheikh Salem, two flash points in southern Yemen's Abyan province, to monitor the truce that was announced earlier in the week, military sources said.
"Observers have begun to be deployed on the ground to monitor the comprehensive ceasefire and separation of forces," the coalition said Wednesday, according to Saudi government TV station Al-Ekhbariya.
"Both parties have affirmed their commitment to respect the ceasefire, to de-escalate and normalise the situation, and to implement the Riyadh Agreement," it added.
Shaqra and Sheikh Salem were the scene of clashes between government troops and southern separatists that raged through Tuesday and into the night, the sources said.
"Our forces in Abyan suffered a violent attack by the invading forces a few hours after the ceasefire came into effect," Nazar Haitham, spokesman for the separatists' Southern Transitional Council (STC), told AFP.
"It is an irresponsible act of the government, which says it is bound by the ceasefire but does not respect it on the ground," he said.
The Yemeni government has not made any statement on the accounts of clashes or the recent takeover in Socotra, however officials have made personal comments on the growing tensions.
Ahmed Bin Daghr, an aide to Yemeni President Abedrabbo Mansour Hadi and a former prime minister, said the war "has achieved nothing of its objectives, destroying Yemen as a state," according to Bloomberg.
"The military option is no longer a viable means," Bin Daghr reportedly said in a statement, calling for direct negotiations to be supervised by the United Nations.
Forces loyal to the Saudi-backed government said they withdrew from the Socotra battle to "de-escalate the situation".
Just a day after Bin Daghr's remarks, Yemen's cabinet demanded authorities on the ground launch reviews of regional and foreign organisations operating in Yemen that are practicing political discord under the cover of charity, the official SABA News Agency reported.
The cabinet confirmed the organisations under review are operating without licenses from relevant authorities, though it failed to name them.
However, a government source revealed to The New Arab's Arabic-language sister platform, Al-Araby Al-Jadeed, that the list includes the UAE's Khalifa Bin Zayed Al-Nahyan Foundation, which has an office on the embattled Socotra island. The organisation does not have offices in any other city in mainland Yemen where the conflict has affected millions of civilians.
Other foreign organisations including some from Turkey, the source revealed.
The move comes just days after Yemen's Minister of Information Mukhtar Al-Rahbi accused the Khalifa Foundation of attempting to "brainwash" young students on the Socotra Island with pro-UAE curriculum at schools.
Yemen In Focus is a regular feature from The New Arab.
Sana Uqba is a journalist at The New Arab.
Follow her on Twitter: @Sanasiino